This file is based on checkout of our SVN repository revision $Revision: 204$https://github.com/obi-bcgo/bcgoChris StoeckertEmily Greenfest-AllenThe ontology is built based on OBI release 2015-04-13Elisabetta ManduchiJie Zhengpreceded byAn example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.http://www.obofoundry.org/ro/#OBO_REL:preceded_byis preceded bypreceded bypreceded_byprecedesprecedesBFO OWL specification labelBFO OWL specification labelReally of interest to developers onlyRelates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.BFO CLIF specification labelBFO CLIF specification labelPerson:Alan RuttenbergReally of interest to developers onlyRelates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2editor preferred labeleditor preferred termeditor preferred termGROUP:OBI:<http://purl.obolibrary.org/obo/obi>PERSON:Daniel SchoberThe concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)editor preferred labeleditor preferred termexample of usageA phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are notGROUP:OBI:<http://purl.obolibrary.org/obo/obi>PERSON:Daniel Schoberexampleexample of usagehas curation statusOBI_0000281PERSON:Alan RuttenbergPERSON:Bill BugPERSON:Melanie Courtothas curation statusdefinitiontextual definitiondefinitiondefinitiondefinition2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. GROUP:OBI:<http://purl.obolibrary.org/obo/obi>The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.definitionPERSON:Daniel SchoberThe official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.definitioneditor noteeditor note1IAO:0000116editor_noteeditor_noteuberonAn administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.GROUP:OBI:<http://purl.obfoundry.org/obo/obi>PERSON:Daniel Schobereditor noteterm editor20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.GROUP:OBI:<http://purl.obolibrary.org/obo/obi>Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several peoplePERSON:Daniel Schoberterm editoralternative termAn alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)GROUP:OBI:<http://purl.obolibrary.org/obo/obi>PERSON:Daniel Schoberalternative termdefinition sourceDiscussion on obo-discuss mailing-list, see http://bit.ly/hgm99wGROUP:OBI:<http://purl.obolibrary.org/obo/obi>PERSON:Daniel Schoberdefinition sourceformal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007has obsolescence reasonPERSON:Alan RuttenbergPERSON:Melanie CourtotRelates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.has obsolescence reasoncurator notescurator note1IAO:0000232curator_notescurator_notesuberonAn administrative note of use for a curator but of no use for a userPERSON:Alan Ruttenbergcurator noteimported fromimported fromFor external terms/classes, the ontology from which the term was importedGROUP:OBI:<http://purl.obolibrary.org/obo/obi>PERSON:Alan RuttenbergPERSON:Melanie Courtotimported fromexpand expression toexpand expression toexpand assertion tofirst order logic expressionelucidationPerson:Barry SmithPrimitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axiomselucidationperson:Alan Ruttenberghas associated axiom(nl)An axiom associated with a term expressed using natural languagePerson:Alan RuttenbergPerson:Alan Ruttenberghas associated axiom(nl)has associated axiom(fol)An axiom expressed in first order logic using CLIF syntaxPerson:Alan RuttenbergPerson:Alan Ruttenberghas associated axiom(fol)has axiom labelterm replaced byAdd as annotation triples in the granting ontologyPerson:Alan RuttenbergPerson:Alan RuttenbergUse on obsolete terms, relating the term to another term that can be used as a substituteterm replaced byISA alternative termRequested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178ISA alternative termPerson: Philippe Rocca-SerraPerson: Alejandra Gonzalez-BeltranISA tools project (http://isa-tools.org)An alternative term used by the ISA tools project (http://isa-tools.org).NIAID GSCID-BRC alternative termAn alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC).NIAID GSCID-BRC alternative termPERSON: Chris Stoeckert, Jie ZhengNIAID GSCID-BRC metadata working groupIEDB alternative termAn alternative term used by the IEDB.IEDBIEDB alternative termPERSON:Randi Vita, Jason Greenbaum, Bjoern Peterstemporal interpretationhttps://code.google.com/p/obo-relations/wiki/ROAndTimetemporal interpretationAbnormal/normal slimAttribute slimcell_qualityDisposition slimPathology slimRelational slim: types of quality that require an additional entity in order to existScalar slimValue slimabstract upper-level terms not directly useful for analysisDescriptionDescriptionAn account of the content of the resource.Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.SourceSourceA reference to a resource from which the present resource
is derived.The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.subset_propertyhas_alternative_idhas_broad_synonymdatabase_cross_referencehas_exact_synonymhas_narrow_synonymhas_obo_namespacehas_related_synonymin_subsetshorthandlabelhas_genetic_background_ofstrain a has genetic backgroud as strain b is that strain a is derived from strain b and genetic make-up (all its alleles at all loci) of strain a is same to strain b except the mutated gene of interest and a very small amount of other genetic material, generally from one or two other strains. For example, the genetic background of the mutant strains NOD.129S7(B6)-Rag1tm1Mom/J (003729) and NOD.Cg-Rag1tm1Mom Prf1tm1Sdz/SzJ (004848) is NOD. Person: Jie Zhengproduces_low_amountPerson: Jie Zhenga produces b if some process that occurs_in a has_output b and amount of b is low relative to normal cases, where a and b are material entities. Examples: defective beta ccell line produces less amount of insulinproduces_high_amounta produces b if some process that occurs_in a has_output b and amount of b is high relative to generally cases, where a and b are material entities. Person: Jie Zhengnot_producePerson: Jie Zhenga produces_no b if some process that occurs_in a and has_no_output b, where a and b are material entities. has contactrelates an entity to a person or an organization that can be contacted for information regarding the entity.has external resourcerelates an entity to the information about it in an external database.has external identifierrelates an entity to an identifier assigned by an external resource which denotes the entity.has email addressPerson: Jie Zhenga instance-level relation between a person or an organization to an email address the person or organization has.executesshortcut relation of a planned process realizes or concretizes some plan specificationhas experimental factorrelates an investigation to an experimental factor which is a study independent variable specified in a study design. An experimental factor can be a material entity (such as treated and untreated specimen), a quality (such as sex of an organism), a process (such as developmental stage of an organism), or an information about a process (such as duration of a treatment), etc.has experimental factor valuerelates experimental factor (could be anything that a study independent variable specification is about) to its values
For example, biological sex can be a study independent variable, potential values can be male or female.value of experimental factorrelates experimental factor values to its factor type (could be anything that a study independent variable specification is about)
For example, male/female could be values for biological sex, 0, 0.01, 0.02 mg/L for glucose concentation, 1,5,20 minutes for treatment duration, etc.examinesrelates an invesitigation to any biologically-related entity that is examined as part of that process, such as a protein, a biological process, etc.associated PubMed IDPerson: Jie Zhenga instance-level relation between an entity to a PubMed ID that denotes a publication associated with the entity.is about organism speciesrelates an information artifact to the species of an organism that it is about.Person: Jie Zhengis denoted byis denoted by is an instance-level, relation obtaining between an entity to an information content entity that is created to specifically refer to something. It is the inverse relation of 'denotes'.Person: Jie Zhengis about genotyperelates an information artifact to the genotype of an organism that it is about.Person: Jie Zhengis about cell type relates an information artifact to the type of a cell that it is about.Person: Jie Zhengis about cell linerelates an information artifact to the cell line that it is about.Person: Jie Zhengis about tissuePerson: Jie Zhengrelates an information artifact to the tissue of an organism that it is about.has gene memberrelates the member (a data item) of a gene list (a data set) to the gene that it is about.is about strainrelates an information artifact to the strain of an organism that it is about.is about phenotyperelates an information artifact to the phenotype born by an organism that it is about.is about development stagerelates an information artifact to the development stage of an organism that it is about.is about treatmentrelates an information artifact to the treatment that it is about. For specimens in an assay, the treatment referred to was performed prior to specimen collection.has durationrelates a process to a time-measurement-datum that represents the duration of the processhas concentrationrelates a molecular entity to its concentration measurement datum that is the measurement of its concentration qualitybinding contextrelates a gene that has protein binding to the biological context in which that binding was identified. differential expression contextrelates a gene that is differentially expressed to the biological context in which that differential expression was identified. context of differential expressionrelates a biological context (e.g., cell, developmental stage, etc.) to a gene whose protein binding was identified in this specific context.context of bindingrelates the context to a gene that protein binding is identified in this specific contextpart ofEverything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimeParthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)
A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.a core relation that holds between a part and its wholehttp://www.obofoundry.org/ro/#OBO_REL:part_ofis part ofmy brain is part of my body (continuant parthood, two material entities)my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)part_ofthis day is part of this year (occurrent parthood)has partEverything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimeParthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.a core relation that holds between a whole and its parthas parthas_partmy body has part my brain (continuant parthood, two material entities)my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)this year has part this day (occurrent parthood)realized inParaphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])is realized byrealized inrealized_inthis disease is realized in this disease coursethis fragility is realized in this shatteringthis investigator role is realized in this investigationrealizesParaphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the processrealizesthis disease course realizes this diseasethis investigation realizes this investigator rolethis shattering realizes this fragilityto say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])preceded byAn example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.http://www.obofoundry.org/ro/#OBO_REL:preceded_byis preceded bypreceded bypreceded_byprecedesprecedesoccurs inParaphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuantb occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at toccurs inoccurs_inunfolds inunfolds_incontains processParaphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at tsite ofhas diseaseJie Zheng, Yongqun He, Yu Lin, Allen Xianghas measurement unit labelhas measurement unit labelis about7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.Smith, Ceusters, Ruttenberg, 2000 years of philosophyThis document is about information artifacts and their representationsis aboutis_about is a (currently) primitive relation that relates an information artifact to an entity.person:Alan Ruttenbergdenotes2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes rA person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogandenotesdenotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specificallyperson:Alan Ruttenbergis quality measurement of8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing laterAlan RuttenbergFrom the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
--
From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]
unit of measure is a quality, e.g. the length of a ruler.
[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]
[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
We have had a long discussion about denotes versus describes.From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.From the second meeting on IAO:
An attempt at defining assay using Barry's "reliability" wording
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate
outputs that describes the input.This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.is quality measurement ofm is a quality measurement of q at t when
q is a quality
there is a measurement process p that has specified output m, a measurement datum, that is about qis duration ofPerson:Alan Ruttenbergis duration ofrelates a process to a time-measurement-datum that represents the duration of the processis_supported_by_dataPhilly 2011 workshopThe relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that processThe relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. is_supported_by_dataOBIOBIhas_specified_input8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.PERSON: Bjoern PetersPERSON: Larry HunterPERSON: Melanie CoutotA relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.PERSON: Alan Ruttenberghas_specified_inputsee is_input_of example_of_usagehas_specified_outputPERSON: Bjoern PetersPERSON: Larry HunterPERSON: Melanie CourtotA relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.PERSON: Alan Ruttenberghas_specified_outputis_manufactured_byAlan RuttenbergLiju Fanc is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.has_makehas_manufacturerhttp://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)is_manufactured_byis_specified_output_ofPERSON:Bjoern PetersA relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.Alan Ruttenbergis_specified_output_ofachieves_planned_objectiveA cell sorting process achieves the objective specification 'material separation objective'BP, AR, PPPB branchPPPB branch derivedThis relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.achieves_planned_objectivemodified according to email thread from 1/23/09 in accordince with DT and PPPB branchhas grainPAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349has grainthe relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard formPERSON: Alan RuttenbergsuppliesA relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.GROUP: Relations branchsupplieshas_supplierA relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.PERSON: Alan RutternbergPERSON: Cristian CocosPERSON: Frank GibsonPERSON: Melanie Courtothas_supplierobjective_achieved_byThis relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.objective_achieved_byOBIOBIis member of organization2009/09/28 Alan Ruttenberg. Fucoidan-use-case2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a populationJZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.Person:Alan RuttenbergPerson:Alan RuttenbergPerson:Helen ParkinsonPerson:Helen ParkinsonRelating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.is member of organizationhas value specificationhas value specificationPERSON: James A. OvertonOBIA relation between an information content entity and a value specification that specifies its value.inheres inA dependent inheres in its bearer at all times for which the dependent exists.a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existenceinheres ininheres_inthis fragility inheres in this vasethis red color inheres in this applebearer ofA bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existencebearer ofbearer_ofis bearer ofthis apple is bearer of this red colorthis vase is bearer of this fragilityparticipates ina relation between a continuant and a process, in which the continuant is somehow involved in the processparticipates inparticipates_inthis blood clot participates in this blood coagulationthis input material (or this output material) participates in this processthis investigator participates in this investigationhas participantHas_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.a relation between a process and a continuant, in which the continuant is somehow involved in the processhas participanthttp://www.obofoundry.org/ro/#OBO_REL:has_participanthas_participantthis blood coagulation has participant this blood clotthis investigation has participant this investigatorthis process has participant this input material (or this output material)is concretized asA journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).concretizesA journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).function ofA function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existencefunction_ofis function ofthis catalysis function is a function of this enzymequality ofA quality inheres in its bearer at all times for which the quality exists.a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existenceis quality ofquality_ofthis red color is a quality of this applerole ofA role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existenceis role ofrole_ofthis investigator role is a role of this personhas functionA bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existencehas_functionthis enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)has qualityA bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existencehas_qualitythis apple has quality this red colorhas roleA bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existencehas_rolethis person has role this investigator role (more colloquially: this person has this role of investigator)derives fromThis is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations.a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entityderives_fromthis cell derives from this parent cell (cell division)this nucleus derives from this parent nucleus (nuclear division)derives intoThis is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entityderives_intothis parent cell derives into this cell (cell division)this parent nucleus derives into this nucleus (nuclear division)location ofMost location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimea relation between two independent continuants, the location and the target, in which the target is entirely within the locationis location oflocation_ofmy head is the location of my brainthis cage is the location of this ratlocated inhttp://www.obofoundry.org/ro/#OBO_REL:located_inLocation as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterusMost location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTimea relation between two independent continuants, the target and the location, in which the target is entirely within the locationlocated inlocated_inmy brain is located in my headthis rat is located in this cage2D boundary of2D_boundary_ofA 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entityboundary ofis 2D boundary ofis boundary ofthe surface of my skin is a 2D boundary of my bodyhas 2D boundaryA 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts.Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape.a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entityhas boundaryhas_2D_boundarymy body has 2D boundary the surface of my skinimmediately preceded bystarts_at_end_ofDavid Osumi-SutherlandX immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)immediately precedesDavid Osumi-Sutherlandends_at_start_ofX immediately_precedes_Y iff: end(X) simultaneous_with start(Y)meetshas plasma membrane part<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)Alexander DiehlLindsay CowellChris MungallEvery B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.PMID:19243617develops fromChris MungallMelissa HaendelDavid Osumi-SutherlandThis is the transitive form of the develops from relationTerry Meehanx develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from ydevelops intoChris MungallDavid Osumi-SutherlandTerry Meehanhas prototypeChris Mungallheart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))capable ofChris MungallPMID:20123131osteoclast SubClassOf 'capable of' some 'bone resorption'mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)RO_0000053 some (RO_0000054 only ?Y)has function realized inPMID:21208450For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. actively participates inagent inx actively participates in y if and only if x participates in y and x realizes some active rolehas active participanthas agentx has participant y if and only if x realizes some active role that inheres in yThis may be obsoleted and replaced by the original 'has agent' relation'heart development' has active development some Shh proteintemporal relationA relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.move to BFO?Allenmember ofis member of is a mereological relation between a item and a collection.An organism that is a member of a population of organismsSIOmember part ofis member ofhas memberhas member is a mereological relation between a collection and an item.SIOhas potential to develop intox has the potential to develop into y iff x develops into y or if x is capable of developing into yproducesMelissa HaendelNote that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue.a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix.produced byMelissa Haendeltranslates_toExample: codon translates_to amino_acid.Inverse of translation _of.Wed Aug 19 00:11:53 PDT 2009kareneilbecktranslation_ofExample: Polypeptide translation_of CDS.Wed Aug 19 00:09:59 PDT 2009X is translation of Y if X is translated by ribosome to create Y.kareneilbeckhas_high_plasma_membrane_amountA relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).has_low_plasma_membrane_amountA relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617).lacks_parthttp://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Ylacks_plasma_membrane_parthttp://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)different_in_magnitude_relative_todifferent_in_magnitude_relative_toq1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.qualityhas_cross_sectionExample: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.has_cross_sectionqualitys3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.increased_in_magnitude_relative_toThis relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.increased_in_magnitude_relative_toq1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.qualityhas NCBI gene iddifferential expression patternhas measurement valuehas measurement valuehas specified valueOBIA relation between a value specification and a number that quantifies it.PERSON: James A. OvertonA range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.has specified valuehas last nameCalled Family Name in vCardfirst namecalled Given Name invCardmouse strainMus musculus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.Person: Jie Zhengrat strainPerson: Jie ZhengRattus norvegicus that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organism.insulin expressing cella cell that expresses a gene for insulin.sequence feature quantificationUPenn GroupPerson: Chris Stoeckert, Jie Zheng, Elisabetta ManduchiA data transformation that attaches quantified values to specific sequence features, e.g. transcript, exon, etc.high throughput sequence alignmentEFO_0004917 high throughput sequence alignment protocola data transformation that aligns sequencing reads to reference sequence.Person: Chris Stoeckert, Jie ZhengTg(Ins1-EGFP/GH1)14Hara mouse strainA mouse strain containing a transgene in which EGFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). Hemizygous mice show expression of EGFP in beta lineage cells of the pancreas.MIP-GFP mouse strainPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRES188 mouse strainSTOCK Tg(Ins1-EGFP/GH1)14Hara/Mmmh mouse strainTg(Ins1-EGFP/GH1)14HaraVanderbilt University Medical CenterC57BL/6 mouse strainA mouse strain that is a laboratory mouse generated from long inbreeding with nearly identical genotype. C57BL/6 mouse has a dark brown, nearly black coat, and an easily irritable temperament. It has a good reproductive performance and is the most widely used "genetic background" for genetically modified mice for use as models of human disease.black 6C57http://en.wikipedia.org/wiki/C57BL/6Person:Jie ZhengC57 black 6functional beta cell like cellA cell that has all features and genetic signatures as functional beta cell. It may not be part of pancreas.Sox17{(GFPCre)Mgn} mouse strainSTOCK Sox17tm2(EGFP/cre)Mgn/Mmnc mouse strainRES1681 mouse strainSox17tm1.3(Cre.GFP)Mgn mouse strainA mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{GFPCre} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a GFP-Cre (Green fluorescent protein-Cre-recombinase) fusion protein into a Sox17 LCA allele thereby replacing Sox17 coding sequences. The Sox17{GFPCre} mice may be used to track Sox17-expressing cells and their early progeny, or to conditionally inactivate genes in Sox17-expressing cells.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSox17{(GFPCre)Mgn}Vanderbilt University Medical CenterPdx1{(CFP)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{tm1.2(CFP)} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a cyan fluorescent protein (CFP, Cerulean), tagged with 3 copies of an SV40 NLS knocked into the endogenous Pdx1 gene. This mouse strain enables pre-pancreatic endoderm to be easily identified in the developing mouse embryo and the isolation of Pdx1(+) cells by FACS.RES1301 mouse strainB6.129S6-Pdx1tm2Mgn/Mmnc mouse strainPdx1CFP mouse strainPdx1{(CFP)Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{tm1Mgn} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create ptf1a{tm1.1(YFP)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). <p>Ptf1a{YFP} mice may be used to visualize yellow fluorescent protein (YFP) expression from the ptf1a allele. Ptf1a is expressedin pancreatic buds beginning at E9.5 andplays a vital role in the growth and lineage specification of pancreatic multipotent progenitor cells (MPCs). Ptf1a is also expressed in the neuronal precursors of the cerebellum, spinal cord, and retina where it also performs fate determining roles.</p>Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm1Mgn}STOCK Ptf1atm1.1Mgn/Mmmh mouse strainptf1aYFP mouse strainRES236 mouse strainVanderbilt University Medical CenterB6.129S-Neurog3{tm1(EGFP)Khk}/Mmcd mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to targeted mutation 1, Klaus H Kaestner (MGI ID: Neurog3{tm1(EGFP)Khk}). A targeted mutation at the Neurogenin 3 locus where EGFP replaces entire coding region of Neurogenin3. The basic phenotype is EGFP expression in developing endocrine cells of pancreas and in glandular regions of the stomach.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe Cartaillerngn3-EGFP mouse strainRES176 mouse strainB6.129S-Neurog3tm1(EGFP)Khk/Mmcd mouse strainB6.129S-Neurog3{tm1(EGFP)Khk}/MmcdVanderbilt University Medical CenterInsm1tm2Mgn mouse strainRES661 mouse strainhttp://www.betacell.org/resource/view/resource_id/661/Person: Jie Zheng, Chris Stoeckerthttp://www.betacell.org/resource/view/resource_id/661/ provide the definition of 'Insm1tm1.1Mgn mouse strain' which might be the early version of 'Insm1tm2Mgn mouse strain'. However, we are not clear the difference between two strains. We borrowed the definition of 'Insm1tm1.1Mgn mouse strain'. In the webpage, it has strain name 'Mouse Strain RES661' and common name 'lnsm1GFP.Cre mouse strain'. We added 'lnsm1GFP.Cre mouse strain' as alternative term which is true to 'Insm1tm2Mgn mouse strain' too .A mouse strain contains a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of the Insm1 gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.Insm1GFP.Cre mouse strainobsolete_STOCK Tg(Tnpo1-EGFP)6729Hara/Mmmh mouse straintruehttp://purl.obolibrary.org/obo/BCGO_0000012http://www.betacell.org/resource/view/resource_id/188/A mouse strain which is hemizygous and shows expression of EGFP in beta lineage cells of the pancreas.RES188 mouse strainPerson: Jie ZhengMIP-GFP mouse strain129X1/SvJ mouse strainA mouse strain that is a laboratory mouse generated from inbreeding. It has white-bellied, pink-eyed, light chinchilla (off-white) or albino or white-bellied, pink-eyed, light chinchilla (light tan). It has a good reproductive performance and is widely used in the production of targeted mutations due to the availability of multiple embryonic stem cell lines derived from them. Person:Jie Zhenghttp://www.informatics.jax.org/mgihome/nomen/strain_129.shtml
http://jaxmice.jax.org/strain/000691.html129X1129/SvJC3H mouse strainA mouse strain that Inbred from F130 to F170 depending on substrain original generated from a cross of a Bagg albino female and a DBA male by Strong in 1920. It has Agouti coat color. Most substrains have a good reproductive performance. It is widely used in a wide variety of research areas including cancer, immunology and inflammation, sensorineural, and cardiovascular biology.Person:Jie Zhenghttp://www.informatics.jax.org/external/festing/mouse/docs/C3H.shtml
http://www.criver.com/EN-US/PRODSERV/BYTYPE/RESMODOVER/RESMOD/Pages/C3HMouse.aspxblack swiss mouse strainPerson: Jie ZhengSox17-expressing definitive endodermal cellPerson: Chris Stoeckert, Jie ZhengChris StoeckertSox17 expressing cell from the embryo body properan endodermal cell that is part of the definitive endoderm and expresses a gene for SOX-17Sox17-expressing Epcam+ pancreatic epithelial cellan epithelial cell that is part of the ventral pancreatic bud, expresses a gene for SOX-17 and has Epcam in the plasma membrane.Person: Chris Stoeckert, Jie ZhengSox17 expressing cell in ventral pancreatic budChris StoeckertPdx1-expressing foregut endodermal cellPdx1-expressing endoderm cellan endodermal cell that is part of the foregut endoderm and expresses the gene for pancreas/duodenum homeobox protein 1Person: Chris Stoeckert, Jie ZhengChris StoeckertPtf1a-expressing multipotent pancreatic cellChris StoeckertPerson: Chris Stoeckert, Jie Zhenga non-terminally differentiated cell that is part of the pancreatic bud, participates in pancreas development and expresses the gene for pancreas transcription factor 1 subunit alpha.Ptf1a-expressing cellPtf1a-lacking pancreatic progenitor cellPtf1a-null cellChris Stoeckerta non-terminally differentiated cell that is part of the pancreatic bud but lacks pancreas transcription factor 1 subunit alpha.Person: Chris Stoeckert, Jie Zhengneurogenin-3-expressing endocrine progenitor cellChris StoeckertNgn3-expressing cella non-terminally differentiated cell that participates in endocrine pancreas developement and expresses the gene for neurogenin-3.Person: Chris Stoeckert, Jie Zhengneurogenin-3-lacking pancreatic progenitor cellChris Stoeckerta non-terminally differentiated cell that is part of the pancreas, participates in pancreas development and lacks neurogenin-3.Ngn3-null cellPerson: Chris Stoeckert, Jie ZhengInsm1-expressing endocrine progenitor cellChris Stoeckerta non-terminally differentiated cell that participates in endocrine pancreas development and expresses a gene for insulinoma-associated protein 1Person: Chris Stoeckert, Jie ZhengInsm1 expressing pancreatic endocrine cellInsm1-lacking endocrine progenitor cellChris StoeckertPerson: Chris Stoeckert, Jie Zhenga non-terminally differentiated cell that is part of the endocrine pancreas and lacks insulinoma-associated protein 1Non-functional Insm1 expressing pancreatic endocrine cellinsulin-expressing immature beta cellChris Stoeckerta type B pancreatic cell that is immature and expresses a gene for insulinPerson: Chris Stoeckert, Jie Zhenginsulin-expressing nascent beta cellsinsulin-expressing mature beta cella type B pancreatic cell that is mature and expresses a gene for insulinChris StoeckertPerson: Chris Stoeckert, Jie Zhenginsulin-expressing mature beta cellsInsm1-expressing Pdx1 high-positive pancreatic endocrine progenitor cellA Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a high level.Person: Jie Zheng, Chris StoeckertInsm1-expressing Pdx1 low-positive pancreatic endocrine progenitor cellPerson: Jie Zheng, Chris StoeckertA Insm1-expressing endocrine progenitor cell that expresses the gene for pancreas/duodenum homeobox protein 1 at a low level.Insm1tm2(GFP.Cre)Mgn/Pdx1tm2(CFP)Mgn mouse strainA mouse strain that is the result of mating between a Insm1GFPCre/+ mouse and a Pdx1CFP/+ mouse both on a CD-1 backgroundPerson: Chris Stoeckert, Anna Osipovichdifferential expression softwareGBCOA software implementing a higher level analysis protocol of type differential expresssion.B6.Cg-Tg(Ins1-EGFP)1Hara/J mouse strainA mouse strain that is genetically modified expressing Enhanced Green Fluorescent Protein (EGFP) under the control of the mouse insulin 1 promoter. Fluorescence is detected in tissues where insulin I is normally expressed; fluorescent protein expression in pancreatic beta-cells is evident from embryonic day (E)13.5 through adulthood. The fluorescence expression pattern is similar to the patterns seen in two other strains STOCK Tg(Ins1-Cerulean)24Hara/J and STOCK Tg(Ins1-DsRed*T4)32Hara/J. This mutant mouse strain exhits normal glucose tolerance and pancreatic insulin levels and may be useful in studies of diabetes and pancreatic beta islet cell biology.Person: Jie Zhenghttp://jaxmice.jax.org/strain/006864.htmlArrayExpress IDA CRID symbol assigned by ArrayExpress to uniquely identify a study in ArrayExpressGEO IDA CRID symbol assigned by Gene Expression Omnibus (GEO) to uniquely identify a study in GEO.cellular marker expressionPerson: Chris Stoeckert, Jie ZhengPenn GroupBeta Cell Biology ConsoritumA gene expression that produces cellular surface proteins that can be used to identify and isolate specific cells.pancreatic materialBeta Cell Biology ConsoritumPerson: Chris Stoeckert, Jie ZhengPenn GroupA material entity that could be whole pancreas, part of pancreas (including a single cell type (e.g., beta cell), or precursor to pancreas.characterization of cell differentiation objectiveA cellular feature identification objective that aims to examine or characterize cell development or differentiation.Person: Chris Stoeckert, Jie ZhengBeta Cell Biology ConsoritumPenn groupcharacterization of differentiation of insulin-producing cells objectiveA characterization of cell differentiation objective that aims to examine the influence of specific protocols with regard to generating insulin-producing cells from putative progenitors or other mechanisms (e.g., transdifferentiation).Beta Cell Biology ConsoritumPenn groupPerson: Chris Stoeckert, Jie Zhengcharacterization of islet/beta-cell stimulation/injury objectivePenn groupBeta Cell Biology ConsoritumPerson: Chris Stoeckert, Jie ZhengA characterization of cell stimulation or injury objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of islets and/or beta-cells to secrete insulin or respond to glucose levels.characterization of pancreas development and growth objectivePenn groupA biological feature identification objective that aims to examine changes in gene expression and/or epigenome during pancreas development or regeneration.Person: Chris Stoeckert, Jie ZhengBeta Cell Biology Consoritumcharacterization of cell stimulation or injury objectiveA cellular feature identification objective that aims to address the effects of compounds, hormones, or cell manipulations on the ability of tissues or specific cell types to perform their normal functions or respond to insult.Beta Cell Biology ConsoritumPenn groupPerson: Chris Stoeckert, Jie Zhengtargets and roles of transcriptional regulators objectiveA molecular feature identification objective that aims to identify genes and processes regulated by transcription factors, co-activators, and other types of transcriptional regulators.Person: Chris Stoeckert, Jie ZhengPenn groupBeta Cell Biology Consoritumtissue expression survey objectivePenn groupPerson: Chris Stoeckert, Jie ZhengA biological feature identification objective that aims to address the question of what genes are expressed in a given tissue or cell type or the expression of genes across multiple cells and tissues.Beta Cell Biology Consoritumepigenetic modification processBeta Cell Biology ConsoritumA biological process of generating epigenetic modifications, such as DNA methylation and histone modifications.Penn GroupPerson: Chris Stoeckert, Jie Zhengislet expansion in vitroPenn GroupBeta Cell Biology ConsoritumA planned process that aims to expand islets in culture and redifferentiate them to insulin producing cells.Person: Chris Stoeckert, Jie Zhengislets in diabetesPerson: Chris Stoeckert, Jie Zhengislet of Langerhans that is part of a person who has diabetes.Will add following axiom after import 'has disease' from CLO
'is part of' some ('Homo sapiens' and 'has disease' some 'diabetes mellitus')Penn GroupBeta Cell Biology Consoritumlong non-coding RNAhttp://en.wikipedia.org/wiki/Long_non-coding_RNABeta Cell Biology ConsoritumPerson: Chris Stoeckert, Jie ZhenglncRNAA ncRNA which is transcribed, non-protein coding, and longer than 200 nucleotides.stress and apoptosis in islets or beta cellsBeta Cell Biology ConsoritumPenn GroupPerson: Chris Stoeckert, Jie Zhengtranscription factor binding site identification by SACO assayTF Binding SACOPerson: Chris Stoeckert, Jie ZhengAn assay that uses chromatin immunoprecipitation combined with serial analysis of chromatin occupancy (SACO) to identify binding sites for transcription factors.Beta Cell Biology ConsoritumPenn grouptranscriptional profiling by MARIS assayMARISPerson: Chris Stoeckert, Jie ZhengAn assay that aims to measure abundance of transcripts using high-quality RNA isolated from cells following intracellular antibody staining and fluorescence-activated cell sorting (FACS).Beta Cell Biology Consoritumhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089459age datumA data item of age. It could be measurement datum like 10 weeks, 2 years, or categorical datum like young, adult.concentration datumA data item of how much of a given substance there is mixed with another substance.Annotations. It could be measurement datum like 10 mM, or categorical datum like low, high concentration.Black and tan, brachyury mouse strainPerson: Jie Zheng, Chris StoeckertBTBRPMID: 25034792, Nephron Exp Nephrol. 2014;126(4):191-5. doi: 10.1159/000363300. "Recent advances in animal models of diabetic nephropathy."A mouse strain that is deficient for the leptin receptor (ob/ob) which is naturally insulin resistant and develops many of the pathological features of human Diabetic nephropathy.large pancreatic ductal cellhttp://www.sciencedirect.com/science/article/pii/S1357272504002717large duct cellPerson: Chris StoeckertA pancreatic ductal cell of the large pancreatic duct.small pancreatic ductal cell'http://www.sciencedirect.com/science/article/pii/S1357272504002717small duct cellPerson: Chris StoeckertA pancreatic ductal cell of a small interlobular pancreatic duct.Tet-On/Ngn3 embryonic stem cellES (Tet-On/Ngn3)Person: Jie Zheng, Chris StoeckertPenn GroupAn embryonic stem cell line that contains a ‘tet-on’ operon system and expresses Ngn3 in the presence of Tetracycline.GKP2 cellAn immortal animal cell line cell which was derived from an insulinoma and expresses insulin and pdx1.GKP2Person: Jie Zheng, Chris StoeckertBCBC (http://www.betacell.org/resource/view/resource_id/1038)GKP4 cellAn immortal animal cell line cell which was derived from a periductal tumor that did not express insulin or pdx1 but expressed genes of the endocrine lineage, such as Isl1 and Nkx2.2.GKP4BCBC (http://www.betacell.org/resource/view/resource_id/1038)Person: Jie Zheng, Chris StoeckertSox17 expressiong H9 cellA H9 cell that expresses Sox17.BCBC (http://www.betacell.org/resource/view/resource_id/4216)Person: Jie Zheng, Chris StoeckertINS-1 (832/1 and 832/2)PMID:17185391Person: Jie Zheng, Chris StoeckertAn INS-1 cell which is poorly responsive to glucose. It is a mixture of INS-1 (832/1) and INS-1 (832/2).INS-1 (832/1) cellPerson: Jie Zheng, Chris StoeckertPMID:17185391An INS-1 cell which is poorly responsive to glucose.INS-1 (832/13 and 833/15)Person: Jie Zheng, Chris StoeckertAn INS-1 cell which is highly responsive to glucose. It is a mixture of INS-1 (832/13) and INS-1 (832/15).PMID:17185391INS-1 (832/13) cellPerson: Jie Zheng, Chris StoeckertAn INS-1 cell which is highly responsive to glucose.PMID:17185391INS-1 (832/2) cellPMID:17185391An INS-1 cellwhich is poorly responsive to glucose.Person: Jie Zheng, Chris StoeckertINS-1 (833/117) cellAn INS-1 cell which is cytokine resistant.Person: Jie Zheng, Chris StoeckertBCBCINS-1 (833/15) cellAn INS-1 cell which is cytokine resistant and highly glucose-responsive.BCBCPerson: Jie Zheng, Chris StoeckertINS-1 (834/40) cellAn INS-1 cell which is cytokine sensitive.BCBCPerson: Jie Zheng, Chris StoeckertINS-1EAn INS-1 cell which has high insulin secretion in responses to glucose.PMID: 10037448Person: Jie Zheng, Chris StoeckertmPAC L20 cellAn immortal animal cell line cell which is a pancreatic duct cell and contains an Ngn3-expressing adenovirus.Person: Jie Zheng, Chris StoeckertmPAC L20PMID: 15340143PANC-1 cellPerson: Jie Zheng, Chris StoeckertPANC-1An immortal animal cell line cell which was established from a pancreatic carcinoma of ductal origin from a 56-year-old Caucasian male. The cell possesses the type B phenotype for G6PD.http://www.sigmaaldrich.com/catalog/product/sigma/87092802R7T1 cellPerson: Jie Zheng, Chris StoeckertPMID: 19164755R7T1An immortal animal cell line cell that is a rat beta-cell line.B6.CBA-{Tg(Gcg-cre)1Herr}/Mmnc mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). <p>A transgenic alteration consisting of a SacI fragment containing the glucagon promoter, inserted at SacI of pBS-beta globin-Cre, resulting in Cre expression in pancreatic lineage cells.</p>B6.CBA-{Tg(Gcg-cre)1Herr}/MmncPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterB6.CBA-{Tg(Ipf1-EGFP)1Herr}/Mmnc mouse strainA mouse strain containing a transgene in which EGFP (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). This strain allows Expression of EGFP in pancreatic precursor populations.B6.CBA-{Tg(Ipf1-EGFP)1Herr}/MmncPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterB6;D2-Tg(Ins-cre)23Herr mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 24505). This strain relies on the recombination of floxed DNA in insulin-producing beta cells.B6;D2-Tg(Ins-cre)23HerrPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterB6;D2-Tg(NEUROG3-cre)1Herr mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). <p>All islet endocrine cells inherit a recombination event, if a segment of DNA is loxP-flanked. Transgene encoding Cre recombinase under the control of a human Neurogenin3 promoter.</p>B6;D2-Tg(NEUROG3-cre)1Herr Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterBX129-Neurod1{tmAK71(lacZ)Jle/Mmcd} mouse strainA mouse strain containing a transgene in which LacZ-Neo (transgene) is driven by the Neurod1 promoter (NCBI Gene ID: 18012). Homozygous phenotype: Postnatal lethal due to neonatal diabetes Pancreas--5% insulin production, no islet formation Gut--no CCK or secretin production Inner ear defects resulting in deafness--no cochlear ganglia and poor vestibular ganglia formation Cerebellar defect resulting in ataxia-- >90% depletion of cerebellar granule cells Hippocampal defects--no dentate gyrus.BX129-Neurod1{tmAK71(lacZ)Jle/Mmcd}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterSTOCK Ipf1{tm1Cvw} mouse strainA mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Global Null) to targeted mutation 1, Christopher V E Wright (MGI ID: Ipf1{tm1Cvw}). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Ipf1{tm1Cvw}Vanderbilt University Medical CenterSTOCK Ipf1{tm2Cvw}/Mmnc mouse strainA mouse strain in which the targeted gene, insulin promoter factor 1, homeodomain transcription factor (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to insulin promoter factor 1, homeodomain transcription factor / targeted mutation 2, Christopher V E Wright (MGI ID: Ipf1{tm2Cvw}). The homozygous phenotype of these animals show growth retardation and dehydration with lack of gastric emptying; ie. a-pancreatic. Heterozygous phenotype includes expression of beta-galactosidase in developing stomach, bile duct and cystic ducts and early pancreatic buds.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Ipf1{tm2Cvw}/MmncVanderbilt University Medical CenterSTOCK Ptf1a{tm1(cre)Cvw} mouse strainA mouse strain in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Gene Replacement) to targeted mutation 1.1, Christopher VE Wright (MGI ID: Ptf1a{tm1.1(cre)Cvw}). <p>Homozygous phenotype is altered pancreatic development with loss of exocrine acini.</p>Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Ptf1a{tm1(cre)Cvw}Vanderbilt University Medical CenterSTOCK Tg(Foxa3-cre)1Khk mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Foxa3 promoter (NCBI Gene ID: 15377). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Tg(Foxa3-cre)1KhkVanderbilt University Medical CenterSTOCK Tg(Ipf1-cre/Esr1)1Dam/Mmcd mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Tg(Ipf1-cre/Esr1)1Dam/MmcdVanderbilt University Medical CenterSTOCK-Tg(Ipf1-cre)89.1Dam/Mmcd mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Ipf1 promoter (NCBI Gene ID: 18609). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK-Tg(Ipf1-cre)89.1Dam/MmcdVanderbilt University Medical CenterSTOCK Tg(Neurog3-cre)1Dam/Mmcd mouse strainA mouse strain containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Tg(Neurog3-cre)1Dam/MmcdVanderbilt University Medical CenterGck{tm3Mgn} mouse strainA mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Gck{tm3Mgn}). This line of mice provides a model for Persistant Hyperinsulinemic Hypoglycemia of Infancy, or PHHI-GK, a rare genetic disease of humans. A gk{A456V} mutation, originally identified in a human pedigree with PHHI-GK, was introduced into these mice by gene knock-in. These mice may be useful for studies of sustained hypoglycemia. The mutation has been bred into a C57BL/6J strain thereby facilitating direct comparisons to both wild type C57BL/6J animals and to animals with a gk{K414E} mutation.Gck{tm3Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGck{tm2Mgn} mouse strainA mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Global Mutation) to targeted mutation 2 (MGI ID: Gck{tm2Mgn}). This line of mice contains a gk{K414E} point mutation that was introduced by gene knock-in. This point mutation wasidentified in aMODY-GK pedigree. These mice will be useful for studies of sustained hyperglycemia since they contain only a single mutation and are congenic with the C57BL/6J strain.Gck{tm2Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGck{tm1.1Mgn} mouse strainA mouse strain in which the targeted gene, Glucokinase (NCBI Gene ID: 103988), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Gck{tm1.1Mgn}). Gk{lox} mice may be used to generate cell specific knock-outs of glucokinase, depending which cre-expressing transgenic mouse is used. In humans, glucokinase gene mutations cause maturity onset diabetes of the young (MODY-GK), a disease that is characterized by early onset and persistent hyperglycemia. Thus, these mice are useful in determining how diminished experssion of glucokinase in specific cells causes hyperglycemia.Gck{tm1.1Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical Centerpck{tm1.1Mgn} mouse strainA mouse strain in which the targeted gene, phosphoenolpyruvate carboxykinase 1 (NCBI Gene ID: 18534), has been modified (allele type: Conditional Null) to targeted mutation 1.1, Mark A Magnuson (MGI ID: Pck1{tm1.1Mgn} ). These mice may be used to study tissue-specific functions of phosphoenolpyruvate carboxykinase (Pck1). This enzyme is essential for gluconeogenesis and also is important for regulating anapleurosis/catapleurosis of TCA cycle intermediates. By generating mice that are homozygous for the pck{lox} allele and that contain a tissue-specific Cre transgene, Pck1 can be deleted from various sites.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical Centerpck{tm1.1Mgn}Rik{tm1.3Mgn} mouse strainA mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Global Null) to targeted mutation 1.3 (MGI ID: 4921505C17Rik{tm2Mgn}). Rictor is an essential part of mTOR complex 2 (mTORC2). mTORC2 phosphorylates Ser473 of Akt/PKB. Eliminating this gene disrupts the function of mTORC2, thereby preventing growth factor mediated activation of Akt/PKB. Thus, these mice have utility for studying both the sites of expression and function of rictor.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRik{tm1.3Mgn}Vanderbilt University Medical CenterRik{tm1.1Mgn} mouse strainA mouse strain in which the targeted gene, Rictor (NCBI Gene ID: 78757), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: 4921505C17Rik{tm1.1Mgn}). These mice carrya conditional allele for Rictor, a component mTOR complex 2 (mTORC2). Disruption of the Rictor gene attenuates phosphorylation ofSer473 of Akt/PKB, which is important for a normal response to growth factor stimulation acting through the PI3-kinase signaling pathway.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRik{tm1.1Mgn}Vanderbilt University Medical CenterPparg{tm1.1Mgn} mouse strainA mouse strain in which the targeted gene, Peroxisome proliferator-activated receptor gamma (NCBI Gene ID: 19016), has been modified (allele type: Conditional Null) to targeted mutation 1.1Mgn (MGI ID: Pparg{tm1.1Mgn}). These mice carry a conditional allele for PPARgamma that can be used in combination with various cre-expressing transgenes.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPparg{tm1.1Mgn}Vanderbilt University Medical CenterB6.129X1-Abcc8{tm1.1Mgn} mouse strainA mouse strain in which the targeted gene, ATP-binding cassette, sub-family C (CFTR/MRP), member 8 (NCBI Gene ID: 20927), has been modified (allele type: Global Null) to targeted mutation 1.1Mgn (MGI ID: Sur1{neotm1.1Mgn}). These mice contain a global knock-out of the sulfonylurea receptor (Sur1), which is part of the ATP-dependent potassium channel. In humans, mutations in Sur1 cause persistent hyperinsulinemic hypoglycemia of infancy (PHHI).B6.129X1-Abcc8{tm1.1Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterTg(Pdx1-Neurog3-ER)1Agb mouse strainA mouse strain containing a transgene in which Neurog3-ER (transgene) is driven by the Pdx1 promoter (NCBI Gene ID: 18609). The transgene is driven by the Pdx1 promoter whcih targets it in pancreas progenitor during development. These mice express a fusion protein between the pro-endocrine transcription factor Ngn3 and the tamoxifen responsive estrogen receptor. An IRES site allows GFP to be co-expressed with Ngn3-ER. The protein is active only upon tamoxifen injection.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerTg(Pdx1-Neurog3-ER)1AgbVanderbilt University Medical CenterGlucagon:rtta mouse strainA mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14562). These mice expresses the rtTA (tetracycline transactivator) in islet alpha cells upon treatment with doxicycline.Glucagon:rttaPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterC57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} mouse strainA mouse strain in which the targeted gene, hypoxanthine guanine phosphoribosyl transferase 1 (NCBI Gene ID: 15452), has been modified (allele type: Gene Replacement) to (MGI ID: ). C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm} carries a transgene encoding the human diphtheria toxin receptor under the control of rat insulin II promoter, was inserted by homologous recombination at the Hprt locus of the X chromosome. It provides a model for depletion of 50% of beta cells using Diphtheria toxin.C57/CBAJ-Hprt{tm3(Ins2-HBEGF)Ugfm}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterB6-Nkx6-1{tm1Msan} mouse strainA mouse strain in which the targeted gene, Nkx6.1 (NCBI Gene ID: 18096), has been modified (allele type: Global Null) to targeted mutation (MGI ID: Nkx6.1{tm1(DsRed2)}). An IRES-DsRed2 cassette was introduced into exon 1 of the Nkx6.1 genomic sequence. The insertion generates a null allele. DsRed2 expression is not detected in these mice.B6-Nkx6-1{tm1Msan}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterTg(RIP-Cre/ESR1){Ydor} mouse strainA mouse strain containing a transgene in which CreER (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). A transgenic mouse expression tamoxifen-inducible Cre recombinase under rat insulin promoter. Upon the injection of tamoxifen, loxP-flanked DNA sequences in beta cells will be deleted.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerTg(RIP-Cre/ESR1){Ydor}Vanderbilt University Medical CenterPtf1a{tm1(tTAoff)Macd} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Mice heterozygous for the tTA replacement of the Ptf1a gene are viable, fertile, of normal size, and do not display any behavioral abnormalities. The replacement places the expression of tTAoff (Gossen &amp; Bujard, PNAS 89:5547, 1992) under the control of the regulatory sequences of the endogenous Ptf1a gene. This mouse was initially designed to be mated to a mouse (see BCBC #M461) bearing a bicistronic Ptf1a-lacZ transgene driven by the tetracycline-regulatory element (TRE: 7 copies of tetO with the CMV minimal promoter). For offspring homozygous for the tTA allele of Ptf1a and hemi- or homozygous for the transgene, the production of PTF1a is due solely to tTA-activation of the transgene, which is repressed by administration of tetracycline/doxycycline. This strategy allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas (similar to that for Pdx1 described in Holland et al., PNAS 99:12236, 2002) and also for the cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and certain defects of the CNS. This tissue-specific expresser of tTA can also be bred with strains bearing other TRE-transgenes for organ-specific conditional expression analyses. Nearly all of the Ptf1a transcription unit has been replaced by a tTAoff coding sequence with accessory translational and RNA-processing signals, as follows, from 5' to 3': the Ptf1a gene transcriptional start and 49-bp of its 5'UTR; the Xenopus laevis beta-globin 5'UTR with Kozak initiator codon; the tTA coding sequence; and a 990-bp rabbit beta-globin gene fragment encoding the last 14-bp of its second exon, the 573-bp second intron, and the 364-bp last exon including a 98-bp 3'UTR with the polyA addition signal and addition site, and 39-bp of 3' beta-globin gene flanking sequence. The Ptf1a locus was modified by recombination-mediated cassette exchange using the cassette exchange allele in Ptf1a-LCA ES cells (Burlison et al., submitted).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm1(tTAoff)Macd}Vanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/Sz mouse strainA mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-Prkdc{scid} IL2rg{null}Tg(Ins2-HBEGF){6832Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 100% of beta cells will be depleted upon administration of diphtheria toxin.NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins2-HBEGF){6832Ugfm}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/Sz mouse strainA mouse strain containing a transgene in which DTR (transgene) is driven by the RIP promoter (NCBI Gene ID: ). NOD-scid IL2rg{null}Hprt{tm3(Ins2-HBEGF)Ugfm} mice are deficient in mature lymphocytes and NK cells, survive beyond 16 months of age, and even after sublethal irradiation resist lymphoma development. They can be induced to become hypoglycemic when Diphtheria toxin is used. 50% of beta cells will be depleted after diphtheria toxin administration.NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}Hprt{tm3(Ins2-HBEGF)Ugfm}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/Sz mouse strainA mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: ). The NOD-Rag1{null} Prf1{null} Ins2{Akita} mouse is the first immunodeficient, spontaneously hyperglycemic mouse strain described that is based on the Ins2{Akita} mutation. This strain is suitable as hosts for human islet and human beta stem and progenitor cell transplantation in the absence of the need for pharmacological induction of diabetes. This strain of mice also has low levels of innate immunity and can be engrafted with a human immune system for the study of human islet allograft rejection.NOD.Cg-Rag1{tm1Mom} Ins2{Akita} Prf1{tm1Sdz}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz mouse strainA mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to (MGI ID: Il2rg{tm1Wjl}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg {null}mice tolerated much higher levels of irradiation conditioning than did NOD-Prkdc{scid} IL2rg {null} mice.NOD.Cg-Rag1{tm1Mom} Il2rg{tm1Wjl}/Sz Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/Sz mouse strainA mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}Tg(Ins1-EGFP/GH1){14Hara}/Sz is a immunodeficient mouse carries a GFP transgene under the control of mouse insulin promoter 1, which leads to expression of eGFP in the beta cells.NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(Ins1-EGFP/GH1){14Hara}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNeurog3{tm1Ggr} mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 1 (MGI ID: Ngn3{EYFP/+}). A targeting construct was designed to insert an IRES-EYFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Coding region for Ngn3 is kept intact consequentely homozygous mice express Ngn3 protein , do not develop diabetes and behave like wild-types. in these mice, Ngn3-positive progenitors express EYFP and can be purified by FACS.Neurog3{tm1Ggr}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterTg(tetO-Ptf1a,lacZ)Macd mouse strainA mouse strain containing a transgene in which bicistronic Ptf1a-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemi- or homozygous for the transgene are viable, fertile, normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat linked to the CMV minimal promoter (collectively the tetracycline-response element). The mice do not express lacZ until a tetracycline-gransactivator (tTA) protein is produced; thereafter Ptf1a and lacZ genes are highly expressed. This mouse was designed to be mated to an apancreatic targeted mutant with tTAoff in place of the Ptf1a coding sequence (see BCBC strain M321). The combined genetic alterations provide normal pancreatic development and function until doxycycline-administration render the mice conditionally null of Ptf1a. This approach allows embryonic developmental arrest at desired stages or cessation of gene function in adult mice for the pancreas, cerebellum, retina, dorsal spinal cord and possibly hypothalamus. This transgenic mouse may be useful in studies of pancreatic endocrine/exocrine development and function, diabetes, and and certain defects of the CNS. This transgenic can also be bred with other tTA strains for conditional mutation analysis.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerTg(tetO-Ptf1a,lacZ)MacdVanderbilt University Medical CenterPtf1a{tm2(W298A)Macd} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(W298A)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse strain has a 2-bp site-directed mutation in the endogenous Ptf1a locus that changes codon 298 from tryptophan to alanine. The mutation disrupts the ability of the PTF1a protein to bind RBPJ. Mice heterozygous for the mutation are viable, fertile, of normal size, and do not display any behavioral abnormalities. Mice homozygous for the mutation phenocopy the homozygous Ptf1a-null. Newborn homozygotes are apancreatic, devoid of the dI4 and dILA GABAergic dorsal interneurons, have an incomplete cerebellum, and die shortly after birth.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm2(W298A)Macd}Vanderbilt University Medical CenterRbpjl{tm1(lacZ)Macd} mouse strainA mouse strain in which the targeted gene, Recombination signal binding protein for immunoglobulin kappa J region-like (NCBI Gene ID: 19668), has been modified (allele type: Global Mutation) to Rbpjl{tm1Macd} (MGI ID: Rbpjl{tm1(lacZ)}). This mouse strain has the Rbpjl gene region spanning exons 7, 8, and 9 replaced with lacZ in-frame. A pgk-neo resistance cassette has been removed by Cre-loxP deletion from the founder. Mice heterozygous and homozygous for the lacZ replacement are viable, fertile, of normal size, and do not display any behavioral abnormalities. In mature mice, the pancreas is one-third smaller than normal, due to less acinar tissue. Expression of the lacZ, measured by bet-galactosidase histostaining is very low.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRbpjl{tm1(lacZ)Macd}Vanderbilt University Medical CenterSTOCK Pdx1{tm1Macd}/J mouse strainA mouse strain in which the targeted gene, Pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Pdx1{tmd1Macd}). Mice homozygous for the targeted mutation fail to develop a pancreas. Heterozygous mice have normal pancreatic development, but have partially impaired glucose tolerance in adulthood. The substitution of the targeted Ipf1/Pdx1 gene with tTAoff inactivates the endogenous allele and places tTAoff expression under the control of the endogenous transcriptional regulatory sequences of the Pdx1 locus. Identical to the endogenous allele, mutant locus expression is detectable in the pancreas and adjacent duodenum but not in other visceral organs or salivary glands. This mutant may be useful to direct tetracycline-regulated expression of responder transgenes in studies of pancreatic endocrine/exocrine development and function and diabetes. This mutant can also be bred with other tetO/TRE strains for pancreas-specific applications. This mutant was originally designed to be mated with mice engineered with a heptameric tetracycline operator (tetO)-controlled bicistronic transgene coding for a normal PDX1 protein and with a beta-galactosidase or EGFP reporter (see BCBC mouse M561). The combined modifications allow normal pancreatic development and function until doxycycline-administration renders the mouse conditionally null of the Pdx1 gene. This configuration for conditional expression of Pdx1is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by tetracycline administration.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Pdx1{tm1Macd}/JVanderbilt University Medical CenterSTOCK Tg(tetO-Pdx1,lacZ)958.1Macd mouse strainA mouse strain containing a transgene in which bicistronic Pdx1-lacZ (transgene) is driven by the TRE promoter (NCBI Gene ID: ). Mice hemizygous and homozygous for the transgenic insert are viable, fertile, of normal size, and do not display any behavioral abnormalities. Expression of the bicistronic transgene is directed by a heptameric tetO repeat fused to a minimal promoter (collectively the tetracycline-response element, or TRE). Transgenic mice do not express lacZ until a tetracycline-transactivator (tTA) protein is introduced; thereafter Pdx1 and lacZ from the transgene are expressed. All cells expressing transgenic Pdx1 coexpress the reporter. Further, mRNA levels of the transgene and endogenous Pdx1 fluctuate in concert during development. This mouse was originally designed to be mated to an apancreatic targeted mutant with the coding sequence of the Pdx1 locus replaced with that for tTAoff (see BCBC #M541). The combined mutations allow normal pancreatic development and function until doxycycline treatments render the mouse conditionally null of the endogenous gene. For this configuration, rescue of pancreatic development is most effective when the transgene locus is homozygous. This allows embryonic developmental arrest at desired stages or cessation of function in adult mice by administration of tetracycline/doxycycline. This transgenic strain may be useful in studies of pancreatic development and endocrine/exocrine function and diabetes. This strain can also be bred with other tTA strains for regulating Pdx1 expression in other contexts.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSTOCK Tg(tetO-Pdx1,lacZ)958.1MacdVanderbilt University Medical CenterNeurog3{tm2(EGFP)Ggr} mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Other) to targeted mutation 2 (MGI ID: Neurog3{tm2(EGFP)Ggr). A targeting construct was designed to insert an IRES-EGFP and a floxed puro downstream of the coding sequence. Crossing with mice expressing Cre in the germ line excised the puromycin resistance gene. Homozygous mice express Ngn3 protein, do not develop diabetes and behave like wild-types. Ngn3-positive cells are labeled with EGFP and can be purified by FACS.Neurog3{tm2(EGFP)Ggr}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterTg(Neurog3-IRES-NLS-LacZ)1Ggr mouse strainA mouse strain containing a transgene in which LacZ (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Transgenic mice where Ngn3-positive cell are labeled with beta-galactosidase. Due to the stability of beta-galactosidase protein, the early descendants of Ngn3-positve cells are also labeled. To generate the Ngn3 promoter::LacZ construct, a 6.86 kb XbaI-XhoI fragment (6696 bp of 5' genomic and untranslated region sequences and 176 bp of ngn3 coding region) of mouse ngn3 genomic DNA was cloned upstream of the IRES-NLS-LacZ-pA sequence in pBS-INL vector resulting in plasmid pngn3(6.8)-INL. The 10.6 kb Ngn3-IRES-NLS-LacZ insert was released by NotI digestion and microinjected into murine oocyte pronuclei, and transgenic line was generated and maintained by crossing into a CD1 outbred background.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerTg(Neurog3-IRES-NLS-LacZ)1GgrVanderbilt University Medical CenterTg(Ins1-mRFP)2Ggr mouse strainA mouse strain containing a transgene in which mRFP (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 1633). These transgenic mice express the monomeric red fluorescent protein under the control of Ins1 gene (BAC) regulatory elements.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerTg(Ins1-mRFP)2GgrVanderbilt University Medical CenterArx{tm1Pgr} mouse strainA mouse strain in which the targeted gene, Arx (NCBI Gene ID: 11878), has been modified (allele type: Gene Replacement) to targeted mutation 1 (MGI ID: Arx{tm1Pgr}). These mice were created by insertion of the LacZ gene (with nuclear localization signal) into the Arx locus by homologous recombination in embryonic stem cells. The Arx gene is localized on the X chromosome. Knockout mice die after birth with due to hypoglycemia. Therefore male mice die at day 2 past birth. The colony has to be propagated with female mice. Arx-deficient mice do not produce alpha cells in the islets of Langerhans.Arx{tm1Pgr}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMafa{tm1.1Rwst} mouse strainA mouse strain in which the targeted gene, v-maf musculoaponeurotic fibrosarcoma oncogene family, protein A (avian) (NCBI Gene ID: 378435), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Mafa{tm1.1(lox)}). Mafa is a basic leucine-zipper containing member of the large Maf transcription factor family.It is part of the RIPE3b1 activator complex and functions as a key activator of insulin and pdx-1 gene transcription. Mafa{lox} mice may be used to generate both global and cell-specific Mafa null mice, depending on which cre-expressing transgenic mouse is used. Removal of Mafa gene might have a profound effect on beta cell function; thus we can closely monitor the expression of islet hormones, transcription functions and the glucose sensing machinery immunohistochemically. The experiment will provide us with the information about the role of Mafa plays in vivo in islet beta cells and the developing pancreas, thus helping us to understand how transcription activator contribute to the pathogenesis and the treatment of diabetes.Mafa{tm1.1Rwst}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMyt1{tm1.1Ggu} mouse strainA mouse strain in which the targeted gene, Myt1 (myelin transcriptioin factor 1) (NCBI Gene ID: 1100535 ), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Myt1{tm1.1Ggu}). Two loxP sites flank exon 6 of Myt1b. The allele behaves as wild type allele without Cre-mediated deletion. Cre-mediated deletion creates null Myt1 allele. The homozygous null is neonatal lethal. Myt1 null pancreas has abnormal islet cell differentiation, ie. single cells produce multiple hormones. Pancreatic-specific Myt1 deletion results in glucose intolerance in males.Myt1{tm1.1Ggu}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterOC-1{tm1.1Mga} mouse strainA mouse strain in which the targeted gene, Onecut1 (NCBI Gene ID: 15379), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: OC-1{tm1.1Mga}). This line of mice allows for conditional inactivation of the OC-1 (HNF6) gene using Cre recombinase. Thus, HNF6 function can be assessed in the different tissues in which it is expressed.OC-1{tm1.1Mga}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2-2{tm3Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2(TNmut) using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). These mice contain mutations in the central core of the Nkx2.2 TN domain (putative groucho-interaction domain).Nkx2-2{tm3Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2-2{tm2Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:rtTA using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The reverse tetracycline transactivator (rtTA) is knocked into the Nkx2.2 coding region, effectively knocking out one Nkx2.2 allele.Nkx2-2{tm2Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterC57/CBAJ-TgN(Glucagon- hHB EGF)Ugfm mouse strainA mouse strain containing a transgene in which Diphtheria Toxin Receptor (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of a rabbit beta-globin intron and the coding sequence of the human diphtheria toxin receptor (heparin-binding epidermal growth factor, membrane form). Downstream, there is a rabbit beta-globin stop codon and the polyadenylation signal.C57/CBAJ-TgN(Glucagon- hHB EGF)UgfmPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterC57/CBAJ-TgN(Glucagon- rtTA)Ugfm mouse strainA mouse strain containing a transgene in which rtTA (transgene) is driven by the Gcg promoter (NCBI Gene ID: 14526). Transgenic strain (generated by pronuclear microinjection) of a transgene containing the rat glucagon promoter (1.6kb fragment) upstream of the coding region of the reverse transactivator doxycycline-dependent. The rtTA is flanked by a rabbit beta-globin intron and downstream there is a stop and polyA signal from the same rabbit beta-globin gene.C57/CBAJ-TgN(Glucagon- rtTA)UgfmPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterC57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm} mouse strainA mouse strain containing a transgene in which DTR (transgene) is driven by the Ins promoter (NCBI Gene ID: 16333). Transgenic mice generated by pronuclear microinjection of a transgene encoding the human diphtheria toxin receptor (heparin binding epidermal growth factor, also termed DTR) under the control of the rat insulin II gene promoter (0.6kb-long fragment). The DTR coding sequence is flanked by the rabbit beta-globin intron and stop/polyA sequences.C57/CBAJ-Tg(Ins2- HBEGF){6832Ugfm}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterFVB/NJ-Tg(MIP-Luc-VU)3Pwrs/J mouse strainA mouse strain containing a transgene in which Luc (transgene) is driven by the MIP promoter (NCBI Gene ID: 16333). We generated a transgenic mouse expressing the luciferase optical reporter under control of the mouse insulin I promoter (MIP-Luc-VU) and characterized this model in mice with increased or decreased beta-cell mass and after islet transplantation. MIP-Luc-VU mice emitted strong and consistent bioluminescence emanating exclusively from beta-cells of the pancreatic islet. MIP-Luc-VU islets had normal islet architecture and secreted insulin normally in vivo and in vitro. By tracking changes in &beta; cell mass using bioluminescence imaging (BLI) and post-mortem metrics, streptozotocin-induced, diabetic MIP-Luc-VU mice had a progressive decline in bioluminescence that correlated with a decrease in pancreatic insulin content and beta-cell mass. MIP-Luc-VU animals fed a high fat diet displayed a progressive increase in bioluminescence that reflected an immunohistochemically verified increase in beta-cell mass. MIP-Luc-VU islets transplanted beneath the renal capsule or into the liver emitted bioluminescence proportional to the number of islets transplanted and graft insulin content and could be imaged for more than a year. Since bioluminescence in the MIP-Luc-VU mouse model is proportional to beta-cell mass in the setting of increased and decreased beta-cell mass and after transplantation, this approach should be useful for non-invasively assessing beta-cell mass in pre-clinical mouse models of glucose homeostasis, beta-cell growth and regeneration, and diabetes.FVB/NJ-Tg(MIP-Luc-VU)3Pwrs/JPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGt(ROSA)26Sor{tm1(Myt1*)Hri} mouse strainA mouse strain in which the targeted gene, ROSA26 (NCBI Gene ID: 14910), has been modified (allele type: Conditional Activating) to ROSA26-loxp-STOP-loxp-Myt1 (MGI ID: Not yet available). Targeted insertion of a LoxP-STOP-LoxP-Myt1 casette into the ROSA26 locus. The presence of Cre recombinase will lead to activation of the 7 zinc finger isoform of Myt1.Gt(ROSA)26Sor{tm1(Myt1*)Hri}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNgn3{tm1(tTA)Hri} mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3 tTA knockin (MGI ID: Ngn3tTA). The mouse contains a Ngn3 knock-in allele. IRES-tTA-rabbit beta globin polyA signal replaced the entire Ngn3 cDNA coding sequence. This is therefore also a Ngn3 null allele. Ngn3 is a bHLH transcription factor that is required for the differentiation of endocrine islet and some neuronal cells.Ngn3{tm1(tTA)Hri}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2-2{tm1Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2:LacZ using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The lacZ gene has been knocked in to the Nkx2.2 genomic locus using RMCE, effectively replacing the two coding exons.Nkx2-2{tm1Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2-2{tm4Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2-NK2 mutation using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). The strain carries a mutant Nkx2.2 allele in which conserved residues of the NK2 domain are mutated to alanines.Nkx2-2{tm4Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{tm6Cvw} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{AIId} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This is a targeted deletion of Area II 5' cis-regulatory region of Pdx1.Pdx1{tm6Cvw}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{tm4Cvw} mouse strainA mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Conditional Null) to targeted mutation 4 (MGI ID: Pdx1{tm4(E2)}). This is a conditional null allele of Pdx1. LoxP sites for Cre recombinase were inserted to flank exon 2 of the gene.Pdx1{tm4Cvw}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{tm2(cre/ESR1)Cvw} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm2(cre/ESR1)} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). CreER knock-in into Ptf1a locus replacing part of the exon1 at the translation initiator ATG position using RMCE method.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm2(cre/ESR1)Cvw}Vanderbilt University Medical CenterPdx1{tm5Cvw} mouse strainA mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Other) to targeted mutation 5 (MGI ID: Pdx1{tm5(AI-II-III)}). LoxP sites for cre recombinase were inserted to flank Area I-II-III, a conserved 5' cis-regulatory region of Pdx1. This allele was shown to be a conditional hypomorph by Fujitani et al. (2006) (PMID 16418487). Pdx1{tm3Cvw} (Pdx1{deltaI-II-III}) is generated by Cre-mediated recombination in the germline of this allele.Pdx1{tm5Cvw}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterDll1{tm1Hri} mouse strainA mouse strain in which the targeted gene, Delta-like 1 (NCBI Gene ID: 13388), has been modified (allele type: Conditional Null) to targeted mutation 1 (MGI ID: Dll1{tm1Hri}). This is a targeted mutation of the Notch ligand Dll1, introducing two loxP sites flanking the exons encoding the DSL domain.Dll1{tm1Hri}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{tm3Cvw} mouse strainA mouse strain in which the targeted gene, Pancreatic and Duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Global Mutation) to targeted mutation 3 (MGI ID: Pdx1{tm3(deltaI-II-III)). Area I-II-III, a conserved 5' cis-regulatory region of Pdx1, was removed by Cre mediated recombination in the germline of Pdx1{tm5Cvw} (Pdx1{Flox123}) by crossing to deleter Cre mice. This allele was shown to be a hypomorph.Pdx1{tm3Cvw}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{tm3Cvw} mouse strainA mouse strain in which the targeted gene, Pancreas Specific Transcription Factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to Targeted Mutation 3 (MGI ID: Ptf1a{tm3Cvw}). This mouse strain is a conditional null allele of Ptf1a. LoxP sites flanking exon 1 and 2 (entire coding region of Ptf1a).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm3Cvw}Vanderbilt University Medical CenterPtf1a{LCA} mouse ESC line A mouse ESC line in which the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Ptf1a{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 4.1 kb region of this gene (including the proximal promoter and both exons 1 and 2) was replaced with a loxP site, an inverted loxP site, and both positive and negative selectable markers. This enables the use of Recombinase-Mediated Cassette Exchange (RMCE) to easily insert various reporter genes or to make other modifications of the Ptf1a gene locus.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{LCA} using the Loxed Cassette Acceptor allele Ptf1a{tm1.1(YFP)}). This ES cell line contains YFP inserted into a Ptf1a{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGck{LCA} mouse ESC line A mouse ESC line in which the targeted gene, glucokinase (NCBI Gene ID: 19213), has been modified (allele type: Cassette Acceptor) to targeted mutation 4 (MGI ID: gk{tm4(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the glucokinase locus by recombinase mediated cassette exchange (RMCE). This LCA uses a loxP/inverted loxP strategy for RMCE and allows sequences between - 6 kb and + 5 kb (relevative to the hepatic-specific promoter) to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterInsm1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Insm1{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor(LCA)allele that may be utilized for the exchange of DNAs of interest into the Insm1 gene locus by recombinase mediated cassette exchange (RMCE). This LCA uses a lox 66/71 and lox 2272 strategy for RMCE and allows a ~5.2 kb region of this single exon gene to be manipulated. This enables a variety of different types of experiments to be performed using a range of cassette designs.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{LCA} mouse ESC line A mouse ESC line in which the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Nkx2.2{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Nkx2.2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox71/66 and Lox2272 strategy for RMCE and allows for manipulation of a 5.1 kb region of the gene (contains promoter, exon 1, and exon 2). This leads to a variety of experiments that can be performed using a wide range of cassette designs.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMIP-GFP mouse ESC line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Ins1 promoter (NCBI Gene ID: 16333). New ESC line derived from MIP-GFP mice (Hara et al. 2003,Am J Physiol Endocrinol Metab. 284: E177-83). Genetic background is C57Bl6/J. When injected into E3.5 mouse blastocysts this line contributes to chimeras and Insulin+/GFP+ double positive cells are found in E14.5 embryonic pancreas. No GFP+ cells are seen outside the pancreas.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNgn3-GFP mouse ESC line A mouse ESC line containing a transgene in which Gfp (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). Mouse ESC line derived from Ngn3-GFP transgenic mice (Gradwohl et al. unpublished). Genetic background is CD1.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{LCA} mouse ESC line A mouse ESC line in which the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Rosa26{tm1(LCA)}). This ES cell line contains a loxed cassette acceptor (LCA) allele in which a 5.17 kb region of the gene has been replaced by a Lox66 site, a puromycin-(delta)-thymidine kinase fusion gene driven by the mouse phosphoglycerol kinase promoter, a kanamycin resistance gene driven by the bacterial EM7 promoter, and a Lox2272 site. These features enable use of Recombinase-Mediated Cassette Exchange for the rapid insertion of various DNAs into the Rosa26 gene locus.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterSox17{LCA} mouse ESC line A mouse ESC line in which the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Sox17{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Sox17 gene locus by recombinase mediated cassette exchange (RMCE). A 3.79 kb region of the gene (exons 3-5) was replaced by tandemly oriented lox66 and lox2272 sites as well as both positive and negative selectable markers.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat IAPP raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "IAPP" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat C-peptide 2 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "C-peptide 2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat C-peptide 1 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "C-peptide 1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse C-peptide 1 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "C-peptide 1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Insulin raised in mouseA monoclonal antibody raised in mouse that targets the human "Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat PDX1 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat PDX1 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat Nkx6.1 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Nkx2.2 raised in goatA polyclonal antibody raised in goat that targets the human "Nkx2.2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human ghrelin raised in goatA polyclonal antibody raised in goat that targets the human "ghrelin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Pax6 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Pax6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human b-catenin raised in goatA polyclonal antibody raised in goat that targets the human "b-catenin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse smooth muscle actin raised in mouseA monoclonal antibody raised in mouse that targets the mouse "smooth muscle actin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human amylase raised in rabbitA polyclonal antibody raised in rabbit that targets the human "amylase" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human c-myc raised in rabbitA polyclonal antibody raised in rabbit that targets the human "c-myc" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat Glut-2 raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "Glut-2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal bovine Carboxypeptidase A raised in rabbitA polyclonal antibody raised in rabbit that targets the bovine "Carboxypeptidase A" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Chromogranin A raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Chromogranin A" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Chromogranin A raised in mouseA monoclonal antibody raised in mouse that targets the human "Chromogranin A" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Cytokeratin 7 raised in mouseA monoclonal antibody raised in mouse that targets the human "Cytokeratin 7" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human PECAM-1 raised in mouseA monoclonal antibody raised in mouse that targets the human "PECAM-1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal aequorea victoria Green Fluorescent Protein raised in rabbitA polyclonal antibody raised in rabbit that targets the aequorea victoria "Green Fluorescent Protein" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal chicken Nkx2.2 raised in mouseA monoclonal antibody raised in mouse that targets the chicken "Nkx2.2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat ghrelin raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "ghrelin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal chicken Islet-1 raised in mouseA monoclonal antibody raised in mouse that targets the chicken "Islet-1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human GATA-4 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "GATA-4" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Glucagon raised in mouseA monoclonal antibody raised in mouse that targets the human "Glucagon" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Somatostatin raised in mouseA monoclonal antibody raised in mouse that targets the human "Somatostatin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Pancreatic Ducts raised in mouseA monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Pancreatic Ducts raised in mouseA monoclonal antibody raised in mouse that targets the rat "Pancreatic Ducts" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Islet Delta Cells raised in ratA monoclonal antibody raised in rat that targets the rat "Islet Delta Cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Pancreatic Ducts raised in ratA monoclonal antibody raised in rat that targets the rat "Pancreatic Ducts" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pro-Insulin raised in mouseA monoclonal antibody raised in mouse that targets the human "Pro-Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ngn3 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ngn3 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Ngn3 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Ngn3 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Nkx6.1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Nkx6.1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Nkx6.1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Nkx6.1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human HNF6 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "HNF6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in goatA polyclonal antibody raised in goat that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in guinea pigA polyclonal antibody raised in guinea pig that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human ghrelin raised in rabbitA polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human ghrelin raised in rabbitA polyclonal antibody raised in rabbit that targets the human "ghrelin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat PDX1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat PDX1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat PDX1 raised in mouseA monoclonal antibody raised in mouse that targets the rat "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Sox2 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Sox2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse FoxA2 raised in goatA polyclonal antibody raised in goat that targets the mouse "FoxA2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human E-cadherin raised in mouseA monoclonal antibody raised in mouse that targets the human "E-cadherin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Sox17 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Sox17" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Sox17 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Sox17" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Sox17 raised in goatA polyclonal antibody raised in goat that targets the human "Sox17" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Shh raised in goatA polyclonal antibody raised in goat that targets the mouse "Shh" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal e. coli beta Galactosidase raised in chickenA polyclonal antibody raised in chicken that targets the e. coli "beta Galactosidase" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal aequorea victoria Green Fluorescent Protein raised in mouseA monoclonal antibody raised in mouse that targets the aequorea victoria "Green Fluorescent Protein" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ptf1a raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Ptf1a" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse IA1 (Insm-1) raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "IA1 (Insm-1)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic duct cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic duct cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic exocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic exocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic exocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic endocrine cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic endocrine cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Alpha cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Alpha cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Definitive Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Definitive Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Definitive Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human T (Brachyury) raised in goatA polyclonal antibody raised in goat that targets the human "T (Brachyury)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Laminin raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Laminin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal chicken Pax6 raised in mouseA monoclonal antibody raised in mouse that targets the chicken "Pax6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterSox17{GFPCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{Cre-GFP} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Using an RMCE strategy, we inserted a Cre-GFP (Green fluorescent protein) fusion protein into a Sox17[LCA] allele thereby replacing Sox17 coding sequences. The Sox17-CreGFP ESCs may be used to track Sox17-expressing cells and their progeny, or to conditionally inactivate genes in Sox17-expressing cells. Mark the expression of Sox17 with both Cre and GFP. Cre will enable lineage tracing using reporter alleles that are activated by cre recombination. GFP will enable direct visualization of Sox17 gene expression.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterInsm1{tm1.1Mgn} mouse strainA mouse strain in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Insm1{tm1.1(GFP-Cre)} using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). <p>Insm1{GFPCre} mice contain a GFP-Cre fusion protein which replaces the Insm1 coding sequence. These mice express green fluorescent protein (GFP) under control of theInsm1gene locus. Insm1 is expressed in pancreatic primordium starting at E9.5. Insm1 is also expressed in neural precursor cells and tumors of may be used for lineage tracing of Insm1-positive cells in both wild-type and Insm1-null mice.</p>Insm1{tm1.1Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGhrl{LCA} mouse ESC line A mouse ESC line in which the targeted gene, Ghrelin (NCBI Gene ID: 58991), has been modified (allele type: Cassette Acceptor) to targeted mutation (MGI ID: Ghrl{LCA}). ES cells were modified by homologous recombination to replace a 6.912 kb region of the Ghrelin (GHRL) gene from 2.7 kb upstream of exon 1 to 0.5 kb downstream of exon 5 with tandemly oriented lox71 and lox2272 sites as well as both positive and negative selectable markers. The gene was replaced by tandemly oriented lox71 and lox2272 sitesas well as both positive and negative selectable markers.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGhrl{Cre-eGFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl{Cre-eGFP} using the Loxed Cassette Acceptor allele Ghrl{LCA}). Recombinase mediated cassette exchange (RMCE) was used to insert the Cre-eGFP fusion protein into the ghrelin locus using ES cells containing the Ghrl{LCA} allele. The Cre-eGFP protein uses the endogenous AUG start codon and polyadenylation sequence.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse BetaTC6 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGt(ROSA)26Sor{tm1(GCK*)Ydor} mouse strainA mouse strain containing a transgene in which GCK (transgene) is driven by the ROSA26 promoter (NCBI Gene ID: 14910). Glucokinase containing the Y214C activating mutation, causing severe persistent hyperinsulinemic hypoglycemia (Diabetes 53:2164-2168, 2004) was targeted to the ROSA26 locus, preceded by a lox-stop-lox sequence and followed by IRES-EGFP.Gt(ROSA)26Sor{tm1(GCK*)Ydor}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat CART raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "CART" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Mo ES-Derived Early Endoderm raised in ratA monoclonal antibody raised in rat that targets the mouse "Mo ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Hu ES-Derived Early Endoderm raised in mouseA monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Hu ES-Derived Early Endoderm raised in mouseA monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Hu ES-Derived Early Endoderm raised in mouseA monoclonal antibody raised in mouse that targets the human "Hu ES-Derived Early Endoderm" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Pancreatic duct cells raised in ratA monoclonal antibody raised in rat that targets the mouse "Pancreatic duct cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Pancreatic duct and acinar cells raised in ratA monoclonal antibody raised in rat that targets the mouse "Pancreatic duct and acinar cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Endothelial cells raised in ratA monoclonal antibody raised in rat that targets the mouse "Endothelial cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse BetaTC6 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse BetaTC6 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "BetaTC6" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Disp2 raised in mouseA monoclonal antibody raised in mouse that targets the human "Disp2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Disp2 raised in mouseA monoclonal antibody raised in mouse that targets the human "Disp2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Lrp11 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Lrp11" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Sez6l2 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Sez6l2 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human DDR1 raised in goatA polyclonal antibody raised in goat that targets the human "DDR1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human DDR1 raised in mouseA monoclonal antibody raised in mouse that targets the human "DDR1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Gpr39-1a raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Gpr39-1a" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat CART raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "CART" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat CART raised in mouseA monoclonal antibody raised in mouse that targets the rat "CART" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-60-DR5-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-228-DR5-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Roas26{R26-228-DR5-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a retinoic acid response element (DR5) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess retinoic acid responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{tm3Macd} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm3Macd} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Modified allele of Ptf1a with a biotinylation Tag sequence attached to the amino terminus of Ptf1a.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm3Macd}Vanderbilt University Medical CenterSox17{tm1.2Mgn} mouse strainA mouse strain in which part or all of the targeted gene, SRY-box containing gene 17 (NCBI Gene ID: 20671) is replaced to create Sox17{CreERT2} using the Loxed Cassette Acceptor allele Sox17{tm1(LCA)}). Sox17{CreERT2} mice may be used either to track Sox17-expressing cells or their progeny or to conditionally inactivate genes in Sox17-expressing cells at specific time points by tamoxifen injection. This line is complementary to Sox17-CreGFP and may avoid possible interferences of expression in the extra-embryonic visceral endoderm. We plan to analyze the effects of a direct activation/deletion of the Wnt pathway in the endoderm by crossing the Sox17-CreERT2 with the gain- and loss-of-function of beta-catenin.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSox17{tm1.2Mgn}Vanderbilt University Medical CenterPolyclonal mouse Carboxypeptidase A1 (CPA1) raised in goatA polyclonal antibody raised in goat that targets the mouse "Carboxypeptidase A1 (CPA1)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Muc1 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Muc1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Cleaved Notch1 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Cleaved Notch1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Jagged1 raised in goatA polyclonal antibody raised in goat that targets the human "Jagged1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{CFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{CFP} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This ES cell line contains cyan fluorescent protein (CFP, Cerulean variant) inserted into a Pdx1{LCA} allele by recombinase mediated cassette exchange. These cells may be useful for identifying pancreatic progenitor cells in cultures that have been stimulated to differentiate towards endodermal and pancreatic fates.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGt(ROSA)26Sor{tm1(Ccnd1T286A)Stang} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(Ccnd1T286A)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This strain expresses both mutant cyclin D1{T286A} and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO). The cyclin D1-T286A mutant cannot be phosphorylated by GSK-3beta and is resistant to polyubiquitination. Therefore, cyclin D1-T286A remains nuclear throughout the cell cycle and has an extended half-life relative to wild-type cyclin D1. This strain represents an effective tool for generating inducible tissue-specific cyclin D1{T286A} mutants with a cherry reporter.Gt(ROSA)26Sor{tm1(Ccnd1T286A)Stang}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.1(R26-DR5-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -60 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm1.1(R26-60-DR5-TA-Cerulean)Mgn}Vanderbilt University Medical CenterNOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/Sz mouse strainA mouse strain in which the targeted gene, recombination activating gene 1 (NCBI Gene ID: 19373), has been modified (allele type: Global Null) to (MGI ID: Rag1{tm1Mom}). Backcrossing of the Rag1 null allele onto the NOD/Lt strain background (NOD-Rag1{null} mice) provided a radio-resistant and longer-lived model for human-cell engraftment. Mutations in X-chromosome-linked Il2rg gene cause X-linked severe combined immunodeficiency (XSCID). Immunodeficient NOD-Rag1{null} IL2rg nullmice tolerated much higher levels of irradiation conditioning than did NOD-Prkdcscid IL2rg{null} mice. This immunodeficient mouse also develops spontaneous hyperglycemia based on the Ins2{Akita} mutation.NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/Sz mouse strainA mouse strain in which the targeted gene, interleukin 2 receptor, gamma chain (NCBI Gene ID: 16186), has been modified (allele type: Global Null) to targeted mutation 1 (MGI ID: Il2rg{tm1Wjl}). NOD-scid IL2rg{null} mice are deficient in mature lymphocytes and NK cells, survive beyond 16-month of age, and even after sublethal irradiation resist lymphoma development. Moreover, cytokine-mobilized human peripheral blood stem cells engraft at high levels in NOD-scid IL2rg{null} mice and develop into human CD3+CD4+ and CD3+CD8+ T cells, Ig+B cells, myeloid cells, NK cells and plasmacytoid dentritic cells.NOD.Cg-Prkdc{scid}Il2rg{tm1Wjl}/SzPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm1.2((R26-228-DR5-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated using RMCE to insert an exchange vector containing a modified Rosa26 promoter linked to a Cerulean fluorescent protein (CFP) reporter gene into mESCs containing a Loxed Cassette Acceptor (LCA) allele within the Rosa26 gene locus. The Rosa26 promoter in this mouse was altered by replacing DNA sequences from -228 to +81 with a multimerized retinoic acid response element (DR5) fused to a TATA box. This mouse will facilitate studies of retinoic acid signaling in an intact animal.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm1.2(R26-228-DR5-TA-Cerulean)Mgn}Vanderbilt University Medical CenterNkx2-2{tm5(null)Suss} mouse strainA mouse strain in which the targeted gene, Nkx2.2 (NCBI Gene ID: 18088), has been modified (allele type: Global Null) to Null (MGI ID: Nkx2.2{tm5(null)}). These mice contain a deletion of the Nkx2.2 coding region to create a null allele.Nkx2-2{tm5(null)Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx6-1{tm2(flox)Msan} mouse strainA mouse strain in which the targeted gene, Nk6 Homeobox 1 (NCBI Gene ID: 18096), has been modified (allele type: Conditional Null) to targeted mutation 1.1 (MGI ID: Nkx6.1{tm1.1Msan}). A conditional allele for nkx6.1 is necessary to study the function of Nkx6.1 in adult mice. A homozygous nkx6.1 null allele results in neonatal lethality due to a paralytic state, which is a direct result of Nkx6.1 function in the development of motor neurons. Conditional loss of Nkx6.1 is achieved through Cre mediated recombination of a floxed exon II of nkx6.1. Our use for a conditional nkx6.1 allele is to study its function in beta cells of the adult pancreas.Nkx6-1{tm2(flox)Msan}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJ mouse strainA mouse strain in which the targeted gene, Perforin 1 (Pore forming protein) (NCBI Gene ID: 18646), has been modified (allele type: Global Null) to (MGI ID: ). Mice that are homozygous for both targeted mutations are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities when housed under specific pathogen free conditions. These double homozygote mutant mice have no mature T or B lymphocytes, no detectable NK cell cytotoxic activity, and lack serum immunoglobulin. The number of nucleated spleen cells is significantly reduced in double mutant mice, when compared to the single homozygote, NOD.129S7(B6)-Rag1tm1Mom/J (Stock No. 003729). Although an increased number of DX5+CD122+ NK cells are found in the spleens of double mutants, these NK cells have impaired cytotoxic activity. The disruption of Prf1 ablates NK cell cytotoxic activity resulting in increased engraftment levels over that observed with Stock No. 003729. All mutant mice develop thymic lymphomas. This double mutant mouse strain may be useful in studies involving engraftment of human hematolymphoid cells.NOD.Cg-Rag1{tm1Mom}Prf1{tm1Sdz}/SzJPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterFoxo1{tm1(DBD)Dac} mouse strainA mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{DBD} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). <p>This line contains a DNA binding-deficient mutant of Foxo1. The mutation may be useful for assessing the contribution of DNA co-activation in the function of Foxo1.</p>Foxo1{tm1(DBD)Dac}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{tm1(Ccnd1)} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ccnd1} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). ES cells express mutant cyclin D1-T286A and a cherry reporter under the regulation of a tetracycline-responsive bi-directional minimal CMV promoter (TRE-Tight; tetO) targeted to the ROSA26 locus.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-60-IBRE4-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-228-IBRE4-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by a BMP response element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These ESCs may be useful for assess BMP responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterFoxo1{tm1(GFP)Dac} mouse strainA mouse strain in which part or all of the targeted gene, forkhead box O1 (NCBI Gene ID: 56458) is replaced to create Foxo1{GFP} using the Loxed Cassette Acceptor allele Foxo1{tm1(LCA)}). A GFP cDNA has been knocked into the Foxo1 locus at the 3' end of the endogenous Foxo1 cDNA to generate a Foxo1-gfp fusion protein that can be used to study Foxo1 translocation in vivo.Foxo1{tm1(GFP)Dac}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse DNER raised in goatA polyclonal antibody raised in goat that targets the mouse "DNER" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Shh raised in mouseA monoclonal antibody raised in mouse that targets the rat "Shh" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal chicken Chick HNF3Beta raised in mouseA monoclonal antibody raised in mouse that targets the chicken "Chick HNF3Beta" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pdx1{tm1(LCA)}). This mouse ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Pdx1 gene locus by recombinase mediated cassette exchange (RMCE). An 8.62 kb region of the gene was replaced by tandemly oriented Lox66 and Lox2272 sites flanking both positive (puromycin) and negative (HSV-TK)selectable markers.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Pax4 raised in guinea pigA polyclonal antibody raised in guinea pig that targets the mouse "Pax4" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN-Cherry-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line expresses mCherry, a red fluorescent protein, under control of the endogenous Rosa26gene. A cassette containing mCherry and other sequences to assure efficient expression were inserted into the Rosa26[LCA] allele by recombinase mediated cassette exchange. These cells will be used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single gene copy and as a reference cell line for fluorescent cell sorting.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNeurog3{tm1.1(nCre)Ggu} mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Gene Replacement) to Ngn3{nCre} (MGI ID: Neurog3{nCre}). A nCre-iRES (n-terminal half of Cre followed by internal ribosomal entry site) was inserted after Ngn3ATG. This allele is confirmed to express both nCre and Ngn3 (no visible phenotype in homozygous animals).Neurog3{tm1.1(nCre)Ggu}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{Non-EN-CFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{LCA} using the Loxed Cassette Acceptor allele Rosa26{tm1.8(Non-EN-CFP)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identifythe optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ngn3 raised in goatA polyclonal antibody raised in goat that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN-CFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN.CFP.SV40.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP.SV40} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26 LCA allele by recombinase mediated cassette exchange. These cells were used to identify the optimal arrangement of regulatory elements for fluorescent protein expression from a single genomic copy.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN-GFP-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.GFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains eGFP inserted into the Rosa26 gene locus. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from a single genomic copy and can serve as a reference cell line for fluorescent cell sorting.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN-CFP-bGpA-Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains CFP (Cerulean) inserted into a Rosa26{LCA} allele by recombinase mediated cassette exchange. These cells were used to identify an optimal combination of regulatory elements for fluorescent protein expression from single a genomic copy.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(Ngn3.CFP)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Ngn3-CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional TetO-regulated fusion gene that has been inserted into a disabled Rosa26 locus. In one direction the tetO/CMV promoter drives expression of CFP (Cerulean). In the other direction it drives Ngn3. Mice containing this allelecan be used to drive the expression of Ngn3 under control of both doxycycline and either an rtTA or tTA transgene.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(Ngn3.CFP)Mgn}Vanderbilt University Medical CenterRosa26{tm1.4(MafA-Cherry)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{MafA-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains a bidirectional Tet0-regulated fusion gene that has been inserted into adisabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives MafA expression.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm1.4(MafA-Cherry)Mgn}Vanderbilt University Medical CenterRosa26{R26-60-3XCNotch-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-60-CNotch-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -228 to +81 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-60-AR8-TA-mCherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-60-AR8-TA-mCherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -60 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporterPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-228-AR8-TA-mCherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.2(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In these cells Rosa26 gene sequences from -228 to +81 were replaced by an Activin response element (AR8) fused to a TATA-mCherry reporter. These ESCs may be usefulto assess Activin, Nodal, and TGFbeta responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{R26-60-6XNotch-TA-Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-60-6XNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{-228.3XCNotch.TA.Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(R26-228-3XCNotch-TA-Cerulean) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The Rosa26 gene sequences from -60 to -228 were replaced with a repeat of alternating 32-bp C-elements and 31-bp Rbpj-binding sites (i.e.,C-R-C-R-C-R). The 31 base-pair region is derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc; uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh, MCB 16:952, 1996). The 32-bp C-element is from the Ela1 enhancer (Kruse et al., MCB 15:4385, 1995).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{-228.6XNotch.TA.Cerulean} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26(Rbpj(R26-228-6XNotch-TA-Cerulean)) using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). The binding site for Rbpj, the transcriptional mediator of Notch signaling was inserted into the Rosa 26 locus replacing nucleotides -60 to -228.The complete insert contains the Rbpj cis element in a series of six repeats. Each repeat includes a 31 base-pair region derived from the CBF1/Rbpj binding region of the C-promoter of EBV (cataaattTTTTCCCACGgcgtgtttacacc). Uppercase letters are the consensus Rbpj binding sequence within the 31-bp element) (Hsieh et al., MCB 16:952, 1996).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Irx2 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Irx2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Arx raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Arx" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterROSA26{(Nkx2.2.CFP)Suss} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{Nkx2.2/CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this strain both CFP and myc-tagged Nkx2.2 were inserted into a ROSA26 LCA allele under control of a bidirectional tetO/CMV promoter element. The mouse line will allow us to explore the contribution of Nkx2.2 to progenitor cell population competency by allowing for the manipulation of Nkx2.2 gene expression within the developing pancreas.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerROSA26{(Nkx2.2.CFP)Suss}Vanderbilt University Medical CenterPolyclonal mouse mArx raised in guinea pigA polyclonal antibody raised in guinea pig that targets the mouse "mArx" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human C-peptide raised in ratA monoclonal antibody raised in rat that targets the human "C-peptide" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(-60.IBRE4.TACerulean)Hri} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{tm2.1(R26-60-IBRE4-TA-Cerulean)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains aBMP reporter element withina modified ROSA26 promoter followed by a CFP reporter. This mouse is identical to the -228 variant except for the amount of ROSA26 DNA.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(-60.IBRE4.TACerulean)Hri}Vanderbilt University Medical CenterPtf1a{rtTA} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{rtTA} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). These mESCs contain the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. rtTA is a transcriptional activator, which can inducibly (in the presence of the tetracycline analog doxycycline) activate the genes under Tet-O activator/promoter element. The rtTA sequences were introduced in to Ptf1a[LCA] by Recombinase-Mediated Cassette Exchange using standard methods.These cells were made in order togenerate a mouse line that express rtTA under control of the Ptf1a gene locus.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{Nepn.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Nepn-Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE usingthe Rosa26.LCA allele. To create a Nepn reporter allele, a 9kb promoter region of the Nepn gene is inserted upstream of the red fluorescent protein mCherry-pA sequence. Since Nepn is expressed during endoderm development, this cell line can be used for visualisation and sorting of endodermal cell populations.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{EN.YFP.bGsplicepA.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{YFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mESCs contain yellow fluorescent protein (YFP, Citrine) under control of the ROSA26 gene locus. They were made as part of a study to quantify variables that affect fluorescent protein expression levels in mESCs. TheYFP sequences are flanked by a translational enhancer and beta-globin splice/polyA sequences. The cassette containing the YFP was inserted intoa ROSA26 LCA allel using Recombinase-Mediated Cassette Exchange.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{Apple.bGsplicepA.Neo} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN.Apple.bGspliceA.neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). To better quantify protein expression levels via confocal microscopy, flow sorting and western blot analysis this cell line contains a 4kb R26 promoter element, Apple (a red fluorescent protein) with an upstream enhancer element, a splicing beta-globin polyA tail and the neomycin gene as a selection agent. Through Recombinase-Mediated Cassette Exchange this construct was inserted into the Rosa26 locus.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{Ngn3.Mafa} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele ). Recombinase mediated cassette exchange was performed to introduce a bidirectional tetO-regulated cassette containing coding sequences for transcription factors MafA and Ngn3 into Rosa26 LCA mESCs. ThismESC line can be used to generate mice that will simultaneously overexpress MafA and Ngn3 using tet-inducible activation with rtTA.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{tm2Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{EN-Cherry-Neo} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line expresses mCherry, a red fluorescent protein, under control of the endogenous ROSA26 gene locus. This mouse was generated as part of a study to identify the optimal combination of regulatory elements for fluorescent protein expression from a single gene copy.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm2Mgn}Vanderbilt University Medical CenterPtf1a{tm2(rtTA)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{tm1.2(rtTA)Mgn} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse line expresses the reverse tetracycline transactivator (rtTA) under control of the Ptf1a regulatory sequences. This mouseisuseful for activating expression of various TetO-regulated genes in sites where Ptf1a is normally expressed.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{tm2(rtTA)Mgn}Vanderbilt University Medical CenterRosa26{(Nepn.Cherry)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26[Nepn.Cherry] using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). Nephrocan (Nepn) has been shown to be expressed specifically during early endoderm development. A Nepn promoter driven reporter (Cherry) has been inserted in the Rosa26LCA locus by recombinase mediated cassette exchange. This mouse line will be useful in visualizing whether Nepn can be used as a specific DE marker for beta-cell development.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(Nepn.Cherry)Mgn}Vanderbilt University Medical CenterRosa26{mIre1.WT.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.WT.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives the wild type form of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allelePerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{mIre1.IG.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Gt(ROSA)26Sor gene trap ROSA 26, Philippe Soriano [ Mus musculus ] (NCBI Gene ID: 14910) is replaced to create Rosa26 LCA using the Loxed Cassette Acceptor allele Rosa26{tm1.1(mlre1.IG.Cherry)FerozPapa}). This mESC line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant version of mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. This cell line should be useful for studying the role of mlre1 in the response to ER stress. By generating mice with this allele tPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(mlre1.WT.Cherry)Fpa} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.WT-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a wild type mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be useful for studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(mlre1.WT.Cherry)Fpa}Vanderbilt University Medical CenterRosa26{(mlre1.IG.Cherry)Fpa} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mlre1.IG-Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains a bidirectional Tet0-regulated fusion gene that has been inserted into a disabled Rosa26 loxed cassette acceptor allele by RMCE. In one direction the tetO/CMV promoter drives expression of a red fluorescent protein (Cherry) while in the other direction it drives a mutant mlre1. mlre1 is an endoplasmic reticulum (ER) membrane kinase response to unfolded protein response (UPR). Activated mlre1 endonucleases leads to the splicing of XBP-1 (a transcription factor which is upregulated in times of ER stress) which transcriptionally increases the expression of ER chaperones and alleviates UPR. These mice may be usefulfor studying the role of mlre1 in the response to ER stress in the setting of diet induced obesity and insulin resistance.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(mlre1.IG.Cherry)Fpa}Vanderbilt University Medical CenterRosa26{(R26-228-IBRE4-TA-Cerulean)Hri} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{R26-228-IBRE4-TA-Cerulean} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). These mice were generated by performing recombinase mediated cassette exchange on the Rosa26 LCA. The sequence from -228 to +81 of the Rosa26 gene was replaced with a BMP responsive element (IBRE4) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in visualizing BMP responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(R26-228-IBRE4-TA-Cerulean)Hri}Vanderbilt University Medical CenterRosa26{Sox9.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9/mCherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of transcription factor Sox9. In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Sox9 and mCherry upon administration of doxycyline when the effector protein rtTA is expressed.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(TetO.Sox9)Msan} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Sox9 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Sox9. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, Sox9 and mCherry will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(TetO.Sox9)Msan}Vanderbilt University Medical CenterRosa26{TetO.NRSF} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, NRSF and mCherry are simultaneously over-expressed upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{tdTOM} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). Recombinase mediated cassette exchange was performed using the Ptf1aLCA. This cell line expresses both tdTOM (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of ptf1a in the adult pancreas. These cells will be useful in a variety of applications such as FACS sorting of ptf1a expressing cells, chromatin immunoprecipitation and proteomic analyses.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human TSPAN7 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "TSPAN7" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human FXYD2 raised in mouseA monoclonal antibody raised in mouse that targets the human "FXYD2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Sez6l2 raised in rabbitA polyclonal antibody raised in rabbit that targets the mouse "Sez6l2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Lrp11 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Lrp11" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Onecut1 raised in guinea pigA polyclonal antibody raised in guinea pig that targets the mouse "Onecut1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{tm3Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create CFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has a cyan fluorescent protein (CFP, Cerulean) expressed under the control of the ROSA26 promoter. The CFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed CFP protein and can be used for transplantation and other experiments where tracing of source cells is required.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm3Mgn}Vanderbilt University Medical CenterRosa26{tm4Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was made by RMCE in the Rosa26[LCA] allele and has yellow fluorescent protein (YFP, Citrine) expressed under control of the ROSA26 promoter. The YFP sequence is preceded by a translational enhancer and followed by intron-containing rabbit beta-globin polyA sequences. This mouse has ubiquitously expressed YFP protein and can be used for transplantation and other experiments where tracing of source cells is required.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{tm4Mgn}Vanderbilt University Medical CenterRosa26{Setd5.GFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this cell line is to study the molecular function of the Setd5 gene.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{(H2B.Apple)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Apple} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). This mouse contains a coding sequence for the mApple-H2B fusion protein in order to tag cells expressing Pdx1 with a red fluorescent protein. The generation of a Pdx-1 red fluorescent marker will enable the isolation of pancreatic lineage progenitors by FACS. The presence of the H2B sequences may also be useful in allowing the plane of cell division to be analyzed.Pdx1{(H2B.Apple)Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNgn3{HA.LCA} mouse ESC line A mouse ESC line in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This ES cell line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterFoxm1{LCA} mouse ESC line A mouse ESC line in which the targeted gene, Forkhead box M1 (NCBI Gene ID: 14235), has been modified (allele type: Gene Replacement) to (MGI ID: ). This ES cell line was made by gene targeting and is designed to serve as a cassette acceptor allele at the Foxm1 locus. The portion of genomic DNA containing exons 2-4 of Foxm1 was flanked with Lox71 and Lox2272 sites and replaced with a selection marker. This line allows for modification of the flanked sequences through RMCE.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{Pdx1.YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the tetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(Pdx1.YFP)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter will drive expression of Pdx1. In the other direction, it will drive the expression of yellow fluorescent protein (YFP). In this mouse line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(Pdx1.YFP)Mgn}Vanderbilt University Medical CenterInsm1{Pdx1.YFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, insulinoma-associated 1 (NCBI Gene ID: 53626) is replaced to create Pdx1/YFP using the Loxed Cassette Acceptor allele Insm1{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Insm1{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor Pdx1. In the other direction, it drives the expression of yellow fluorescent protein (YFP). In this cell line, when the effector protein rtTA is expressed, Pdx1 and YFP will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{3TF.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of the red fluorescent protein mCherry. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(3TF.Cherry)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create mCherry/MafA/Pdx1/Ngn3 using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] by RMCE. In one direction, the TetO/CMV promoter drives expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 linked by 2A peptide cleavage sequences. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, all three transcription factors and mCherry will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(3TF.Cherry)Mgn}Vanderbilt University Medical CenterPdx1{AIVd} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{aIVd} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this ES cell line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1{LCA} allele. This cell line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{(AIVd)Rwst} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{area IV deletion} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, Area IV of the Pdx1 enhancer (-2168/-1913 relative to the primary transcription start site) was deleted using RMCE in the Pdx1[LCA] allele. This mouse line allows for assessment of the role of these DNA sequences in the regulation and function of Pdx1.Pdx1{(AIVd)Rwst}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{cCre-Knock-in} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, the sequence for one of the two bi-partite Cre molecules (cCre) and the IRES sequence were knocked into a site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2{LCA} allele. The presence of the IRES sequence allows for the transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This results in the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{(Cre-Knock-in)} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-knock-in)} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, one of the two bi-partite Cre molecules, cCre, together with the IRES sequence was knocked into the site directly upstream of the Nkx2.2 start codon using RMCE in the Nkx2.2[LCA] allele. The presence of the IRES sequence allows for transcription of cCre and Nkx2.2 from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Nkx2.2{(Cre-Knock-in)}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{3XHA.Nkx2.2} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this cell line RMCE in the Nkx2.2.LCA allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{(3XHA.Nkx2.2)Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{3XHA-Nkx2.2} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse line, RMCE in the Nkx2.2{LCA} allele was used to introduce a triple HA tag in frame at the N-terminus of the transcription factor Nkx2.2. This allows for efficient immunoprecipitation of HA-tagged Nkx2.2 protein from mouse tissues to perform ChIP and protein-protein interaction studies.Nkx2.2{(3XHA.Nkx2.2)Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{Cre.EGFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell line, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{(Cre-ER)} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1[LCA] allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells.Pdx1{(Cre-ER)}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Cherry using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this ES cell, 1.956 kb of the native Nkx2.2 gene, containing a portion of exon 1 (all but the first 214 bp) and all of exon 2, was replaced by the mCherry cassette in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression in the mouse to be identified using direct immunofluorescence and FACS purification of Nkx2.2 expressing cells.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal enterobacteria phage p1 Cre raised in guinea pigA polyclonal antibody raised in guinea pig that targets the enterobacteria phage p1 "Cre" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPax4{HA.LCA} mouse ESC line A mouse ESC line in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This ES cell line is made by gene targeting and is designed to express an HA-tagged version of the transcription factor Pax4. Lox71 and Lox2272 sites are inserted, flanking the last coding exon of the Pax4 gene. In the flanked region, an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for future manipulations of the flanked region by RMCE.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human CDCP1 raised in goatA polyclonal antibody raised in goat that targets the human "CDCP1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human CD-200 raised in goatA polyclonal antibody raised in goat that targets the human "CD-200" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Coagulation factor 3(rhF3) raised in goatA polyclonal antibody raised in goat that targets the human "Coagulation factor 3(rhF3)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Ngn3 raised in sheepA polyclonal antibody raised in sheep that targets the human "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Pax4 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Pax4 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal mouse Pax4 raised in mouseA monoclonal antibody raised in mouse that targets the mouse "Pax4" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human CD142 raised in mouseA monoclonal antibody raised in mouse that targets the human "CD142" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Beta cell, IC2 raised in ratA monoclonal antibody raised in rat that targets the rat "Beta cell, IC2" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human CD-200 raised in goatA polyclonal antibody raised in goat that targets the human "CD-200" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJ mouse strainA mouse strain in which the targeted gene, protein kinase, DNA activated, catalytic polypeptide (NCBI Gene ID: 19090), has been modified (allele type: Other) to severe combined immunodeficiency (MGI ID: Prkdc{scid}). The NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, commonly known as NOD scid gamma (NSG), do not express the Prkdc gene nor the X-linked Il2rg gene. NSG mice are viable, fertile, normal in size and do not display any gross physical or behavioral abnormalities. Histological examination of lymphoid tissues reveals absence of lymphoid cells and some cystic structures in the thymus, an absence of follicles in the spleen and markedly diminished celluarity of lymph nodes. NSG mice are deficient in mature lymphocytes, serum Ig is not detectable and natural killer (NK) cell cytotoxic activity is extremely low. These mice are resistant to lymphoma development even after sublethal irradiation treatment. These mutant mice have been shown to readily support engraftment of human CD34+ hematopoietic stem cells and represent a superior, long-lived model suitable for studies employing xenotransplantation strategies. Please note that the NSG carries the true null interleukin-2 receptor gamma chain mutation and should not be confused with other strains that express a truncated interleukin-2 receptor gamma chain as described in: "Modulation of hematopoiesis in mice with a truncated mutant of the interleukin-2 receptor gamma chain".NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl}/SzJPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJ mouse strainA mouse strain in which the targeted gene, insulin II (NCBI Gene ID: 16334), has been modified (allele type: Other) to Akita (MGI ID: Ins2{Akita}). NRG-Akita mice, which are homozygous for the Rag1tm1Mom and the Il2rgtm1Wjl alleles (males are hemizygous for the X-linked Il2rgtm1Wjl allele) and heterozygous for the Ins2Akita allele, develop spontaneous hyperglycermia. No mature T, B or NK cells are detected in flow cytometric analysis of splenocytes from NRG-Akita mutant mice. Granulocyte and macrophage populations are similar to those seen in NRG mice. NRG-Akita mice develop hyperglycemia between 3 and 5 weeks of age. Histological examination at 3 weeks of age reveals normal pancreas morphology, and routine insulin and glucagon staining. By approximately 32 weeks of age, NRG-Akita mice display disorganized, condensed pancreatic islet architecture, with loss of insulin-positive cells. Euglycemia is restored by subrenal transplantation of mouse or human islets or intrapancreatic transplantation of dissociated mouse islet cells. NRG-Akita mice engrafted with human hematopoietic stem cells (HSC) develop humanized immune systems. Approximately 60% of the human HSC engrafted NRG-Akita mice reject human islet allografts.NOD.Cg-Rag1{tm1Mom}Ins2{Akita}Il2rg{tm1Wjl}/SzJPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{Cre.ER} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre-ER using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, the first exon of the transcription factor Pdx1 was replaced with the coding sequence for a Cre-ER fusion protein using RMCE in the Pdx1{LCA} allele. Pdx1-promoter driven Cre-ER expressing mice enable tamoxifen-inducible Cre-LoxP manipulation of pancreatic lineage cells.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNgn3{(HA.LCA)} mouse strainA mouse strain in which the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925), has been modified (allele type: Cassette Acceptor) to (MGI ID: ). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Ngn3. The Lox71 and Lox2272 sites were inserted flanking the Ngn3 coding sequence. Within the flanked region an HA-tag was placed at the N-terminus of the Ngn3 protein. This allele can be used to study chromatin and protein-protein interactions of Ngn3. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE.Ngn3{(HA.LCA)}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPax4{(HA.LCA)Ggu} mouse strainA mouse strain in which the targeted gene, paired box 4 (NCBI Gene ID: 18506), has been modified (allele type: Cassette Acceptor) to targeted mutation 1 (MGI ID: Pax4{tm1(LCA)Ggu}). This mouse line was made by gene targeting and designed to express an HA-tagged version of the transcription factor Pax4. The Lox71 and Lox2272 sites were inserted flanking the last coding exon of the Pax4 gene. Within the flanked region an HA-tag was placed at the C-terminus of the PAX4 protein. This allele can be used to study chromatin and protein-protein interactions of PAX4. Additionally, the Lox71 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future.Pax4{(HA.LCA)Ggu}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(Setd5.GFP)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Setd5/GFP using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. A coding sequence for green fluorescent protein (GFP) was inserted into the first exon of the Setd5 gene. This exon is located upstream of the Rosa26 transcribed sequence and is transcribed in an opposite orientation. The GFP-polyA cassette, transcribed from the Setd5 promoter, knocks out Setd5 transcription and provides a reporter for Setd5 gene expression. The purpose of this mouse line is to study the molecular function of the Setd5 gene.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(Setd5.GFP)Mgn}Vanderbilt University Medical CenterRosa26{228.TOP.CFP} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 7xTcf/Lef binding site using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES cell line was generated by RMCE in the Rosa26{LCA} allele. The Rosa26 gene sequence (from -228 to +81) was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. This ES cell line may be useful for assessing canonical Wnt responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPtf1a{(tdTomato)} mouse strainA mouse strain in which part or all of the targeted gene, pancreas specific transcription factor, 1a (NCBI Gene ID: 19213) is replaced to create Ptf1a{td.TOM} using the Loxed Cassette Acceptor allele Ptf1a{tm1(LCA)}). This mouse cell line was generated by RMCE in the Ptf1a[LCA] allele. Pancreata of this mouse line express both td.Tomato (a red fluorescent protein) and an N-terminal epitope tagged Strep/Flag (NSF) fusion of the transcription factor Ptf1a. This line may be used in a variety of applications such as FACS sorting of Ptf1a expressing cells, chromatin immunoprecipitation, and proteomic analyses.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerPtf1a{(tdTomato)}Vanderbilt University Medical CenterNkx2.2{(Cre.EGFP)Suss} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{Cre-EGFP} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this mouse, a coding portion of the transcription factor Nkx2.2 was replaced with a Cre-EGFP cassette, in frame to the Nkx2.2 ATG. This allows for sites of Nkx2.2 gene expression to be identified in mice using direct immunofluorescence, FACS purification of Nkx2.2 expressing cells, and lineage tracing using Nkx2.2 driven Cre expression.Nkx2.2{(Cre.EGFP)Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{(TetO.NRSF)Msan} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create NRSF using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line contains bidirectional TetO-regulated genes inserted into the Rosa26[LCA] allele by RMCE. In one direction, the TetO/CMV promoter drives the expression of the transcription factor NRSF/REST. In the other direction, it drives the expression of red fluorescent protein mCherry. In this mouse line, when the effector protein rtTA is expressed, NRSF and mCherry will be simultaneously over-expressed upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{(TetO.NRSF)Msan}Vanderbilt University Medical CenterGt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{(R26-228-AR8-TA-mCherry)} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse line was generated by RMCE in the Rosa26[LCA] allele. In this mouse line, the Rosa26 gene sequence (-228 to +81) was replaced by the Foxh1/Smad2-dependent, Mix2-derived Activin response element (AR8) fused to a TATA-mCherry reporter. These mice may be useful to assess Activin, Nodal, and TGFbeta responsiveness.Gt(ROSA)26Sor{tm2.1(mix1b-mCherry)Mgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNepn{Cherry} mouse ESC line A mouse ESC line in which the targeted gene, Nephrocan (NCBI Gene ID: 66650), has been modified (allele type: Global Null) to (MGI ID: Neph(mCherry)). This ES cell line was made by gene targeting and was designed to express red fluorescent protein (mCherry) from the Nepn promoter thereby disrupting the expression of Nepn. The FP coding sequence was inserted dowstream of the Nepn start codon, in front of the Nepn first exon. This cell line is used to study the function and expression of Nepn.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterIns2{Apple.LCA} mouse ESC line A mouse ESC line in which the targeted gene, Insulin 2 (NCBI Gene ID: 20671), has been modified (allele type: Cassette Acceptor) to (MGI ID: Ins2{(apple.LCA)}). This ES cell line was made by gene targeting and designed to express a H2B-Apple fusion protein (nuclear red fluorescent protein) from the Ins2 promoter. The FP coding sequence is downsteam of the Ins2 start codon (replacing exon 2 of Ins2) and is flanked by Lox66/Lox2272 sites to allow for future manipulations of the flanked region by RMCE.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{rTTA} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{rTTA} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for rTTA protein, using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven rTTA expressing mice will enable tetracycline-inducible manipulation of pancreatic lineage cells.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{Cre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1/cre using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this cell line, thefirst exon of Pdx1 was replaced with the coding sequence for Cre-recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx1-promoter driven Cre-expressing cells will enable Cre-LoxP manipulation of pancreatic lineage cells.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{228.3TF.GFP.Cre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create 3TF.GFP-Cre using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This cell line contains TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. The TetO/miniCMV promoter was placed (at -228) upstream of the putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with a GFP-Cre fusion protein. The sequences are linked by 2A peptide cleavage sequences. In this cell line, when the effector protein rtTA is expressed, all three transcription factors and GFP-Cre will be over-expressed simultaneously upon administration of doxycyline.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{mIre1.N906A.Cherry} mouse ESC line A mouse ESC line in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{mIre1.N906A.Cherry} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This ES line contains bidirectional TetO-regulated genes inserted into the Rosa26{LCA} allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant(N906A) of IRE1, an ER transmenbrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This ES cell line can be used to simultaneously over-express Ire1(N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance. Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human HIP-14 ZDHHC17 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "HIP-14 ZDHHC17" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterGhrl{tm1(Cre-eGFP)Suss} mouse strainA mouse strain in which part or all of the targeted gene, Ghrelin (NCBI Gene ID: 58991) is replaced to create Ghrl Cre-eGFP CEV using the Loxed Cassette Acceptor allele Ghrl{LCA}). Ghrl{Cre-eGGP} mice contain a Cre-eGFP fusion protein which replaces the Ghrelin coding sequence. These mice expressc Cre-eGFP phusion protein under control of the Ghrelin gene locus. The Ghrl{Cre-eGGP} mice may be used to track ghrelin-expressing cells progeny,or to conditionally inactivate genes in ghrelin-expressing cells.Ghrl{tm1(Cre-eGFP)Suss}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Cd31 (PECAM1) raised in mouseA monoclonal antibody raised in mouse that targets the human "Cd31 (PECAM1)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal cow GFAP raised in rabbitA polyclonal antibody raised in rabbit that targets the cow "GFAP" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Glucagon (GCG) raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Glucagon (GCG)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Glucagon (GCG) raised in guinea pigA polyclonal antibody raised in guinea pig that targets the human "Glucagon (GCG)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal pig Insulin raised in guinea pigA polyclonal antibody raised in guinea pig that targets the pig "Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Ki67 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Ki67" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human MafA raised in rabbitA polyclonal antibody raised in rabbit that targets the human "MafA" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human MafB raised in rabbitA polyclonal antibody raised in rabbit that targets the human "MafB" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Pancreatic Polypeptide (PPY) raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Pancreatic Polypeptide (PPY)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Somatostatin (Sst) raised in sheepA polyclonal antibody raised in sheep that targets the human "Somatostatin (Sst)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal rat Tuj1 (TUBB3) raised in rabbitA monoclonal antibody raised in rabbit that targets the rat "Tuj1 (TUBB3)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat VEGFA raised in goatA polyclonal antibody raised in goat that targets the rat "VEGFA" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Foxa2 (HNF3b) raised in goatA polyclonal antibody raised in goat that targets the mouse "Foxa2 (HNF3b)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Muc1 raised in hamster (armenian)A monoclonal antibody raised in hamster (armenian) that targets the human "Muc1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human HNF-1β raised in goatA polyclonal antibody raised in goat that targets the human "HNF-1β" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Sox9 raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Sox9" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human CDCP1 raised in goatA polyclonal antibody raised in goat that targets the human "CDCP1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human α-Amylase (AMY2A) raised in rabbitA polyclonal antibody raised in rabbit that targets the human "α-Amylase (AMY2A)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal cow Insulin raised in guinea pigA polyclonal antibody raised in guinea pig that targets the cow "Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Insulin raised in guinea pigA polyclonal antibody raised in guinea pig that targets the human "Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Insulin raised in goatA polyclonal antibody raised in goat that targets the human "Insulin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Glucagon raised in rabbitA polyclonal antibody raised in rabbit that targets the human "Glucagon" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal human Somatostatin (Sst) raised in goatA polyclonal antibody raised in goat that targets the human "Somatostatin (Sst)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal rat Synaptophysin (SYP) raised in rabbitA polyclonal antibody raised in rabbit that targets the rat "Synaptophysin (SYP)" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNgn3{T2A.nCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse ES cell line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3.HA.LCA ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from Ngn3 promoter. This mouse line, in combination with Nkx2.2-cCre mouse line, allows to label pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{T2A.cCre} mouse ESC line A mouse ESC line in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is inserted downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2{LCA}allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. Mouse lines obtained from these ES cells allow the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNeurog3{Cre-ER.BAC} mouse ESC line A mouse ESC line containing a transgene in which Cre (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.Cre-ER.LCA BAC transgene inserted in a genome. The transgene is designed to express Cre-ER under control of Neurog 3 promoter and will allow inducible tracking or gene inactivation in the Ngn3-LOW and Ngn3-HIGH populations of pre-endocrine cells. Additionally, the lox66 and lox2272 sites will allow the BAC transgene to serve as a loxed cassette acceptor (LCA) in ES cells for future recombinase-mediated cassette exchange (RMCE).Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{CreMgn} mouse strainA mouse strain in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{Cre} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this mouse strain, the first exon of Pdx1 is replaced with coding sequence for Cre recombinase using RMCE in the Pdx1{LCA} allele. Generation of Pdx-promoter driven Cre expressing mice will enable Cre-LoxP manipulation of pancreatic lineage cells.Pdx1{CreMgn}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{228.TOP.CFPHri} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26{228.TOP.CFP} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). In this mouse strain the Rosa26 gene sequence from -228 to +81 was replaced by a Wnt response element (7xTcf/Lef binding site) fused to a TATA-Cerulean (CFP) reporter. These mice may be useful in assessing Canonical Wnt responsiveness.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{228.TOP.CFPHri}Vanderbilt University Medical CenterNeurog3{RG.BAC} mouse ESC line A mouse ESC line containing a transgene in which RG (transgene) is driven by the Neurog3 promoter (NCBI Gene ID: 11925). This line has a single copy of Neurog3.RG.LCA BAC transgene inserted in the genome. The transgene is designed to express an H2B-mCherry fusion protein in the nucleus and a membrane anchored EGFP (via GPI), both under the control of the Neurog3 promoter. This will allow for live-cell imaging of mitotic nuclear/chromosome dynamics and membrane protrusive behavior in endocrine progenitors. Additionally, Lox71 and Lox2272 sites flanking the transgene will allow for manipulations by RMCE in the future.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{228.3TF.GFP-CreMgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create ROSA26{228.3TF.GFP-Cre} using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse strain contains TetO-regulated genes inserted into the Rosa 26{LCA} allele by RMCE. TetO/miniCMV promoter is placed at -228 position upstream of putative ROSA26 transcription start site and drives the expression of a polycistronic mRNA with transcription factors MafA, Pdx1, and Ngn3 together with GFP-Cre fusion protein linked by 2A peptide cleavage sequences. These mice will be able to simultaneously over-express all three transcription factors and GFP-Cre upon administration of doxycyline when the effector protein rtTA is expressed.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{228.3TF.GFP-CreMgn}Vanderbilt University Medical CenterNgn3{T2A.nCreGgu} mouse strainA mouse strain in which part or all of the targeted gene, Neurogenin 3 (NCBI Gene ID: 11925) is replaced to create Ngn3{T2A.nCre} using the Loxed Cassette Acceptor allele ). In this mouse line, one of the two bi-partite Cre molecules, nCre, was knocked in upstream of Ngn3 coding sequence by RMCE in Ngn3{HA.LCA} ES cell line. nCre sequence is expressed from policistronic mRNA linked by 2a peptide to Ngn3 coding sequence allowing for simultanious expression of both proteins from the Ngn3 promoter. This mouse line, in combination with Nkx2.2{cCre} mouse line, allows for the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Ngn3{T2A.nCreGgu}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPdx1{H2B.Neptune} mouse ESC line A mouse ESC line in which part or all of the targeted gene, pancreatic and duodenal homeobox 1 (NCBI Gene ID: 18609) is replaced to create Pdx1{H2B.Neptune} using the Loxed Cassette Acceptor allele Pdx1{tm1(LCA)}). In this line, the first exon of Pdx1 is replaced with coding sequence for mNeptune (a far red fluorescent protein) using RMCE in the Pdx1 LCA allele. Generation of a Pdx-promoter driven mNeptune fluorescent allele will enable the isolation of pancreatic lineage cells by FACS and broaden the possibilities for combinatorial sorting with other fluorescent alleles.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterSst.rTTA.LCA mouse ESC line A mouse ESC line in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Cassette Acceptor) to Sst.rTTA loxed cassette acceptor (MGI ID: Sst.rTTA{LCA}). This allelle is designed to express a tet-inducible reverse-transactivator under control of the somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete replaces Sst coding exons (I and II). The allele can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterFoxa2{LCA} mouse ESC line A mouse ESC line in which the targeted gene, forkhead box A2 (NCBI Gene ID: 15376), has been modified (allele type: Cassette Acceptor) to Forkhead box A2 loxed cassette acceptor (MGI ID: Foxa2{LCA}). This ES cell line contains a loxed cassette acceptor (LCA) allele that may be utilized for the exchange of DNAs of interest into the Foxa2 locus by recombinase mediated cassette exchange (RMCE). This LCA uses a Lox66/71 and Lox2272 strategy for RMCE and allows for manipulation of a 4.7 kb region of the gene (contains a promoter and all exons: exon 1, 2 and 3). This leads to a variety of experiments that can be performed using a wide range of cassette designs.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ngn3 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Ngn3 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Ngn3" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Nkx6.1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Nkx6.1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Nkx6.1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse PDX1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "PDX1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Prox1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterPolyclonal mouse Prox1 raised in chickenA polyclonal antibody raised in chicken that targets the mouse "Prox1" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNkx2.2{T2A.cCreGgu} mouse strainA mouse strain in which part or all of the targeted gene, NK2 transcription factor related, locus 2 (NCBI Gene ID: 18088) is replaced to create Nkx2.2{T2A.cCre} using the Loxed Cassette Acceptor allele Nkx2.2{tm1(LCA)}). In this line, one of the two bi-partite Cre molecules, cCre, is placed downstream of Nkx2.2 coding sequence fused with 2a peptide using RMCE in the Nkx2.2[LCA] allele. The presence of the T2A sequence allows for transcription of Nkx2.2 and cCre from the native Nkx2.2 locus at the same time. This mouse line allows the labeling of pancreatic epithelium cells that co-express high levels of Ngn3 and Nkx2.2 during mouse embryonic development.Nkx2.2{T2A.cCreGgu}Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterRosa26{mIre1.N906A.CherryMgn} mouse strainA mouse strain in which part or all of the targeted gene, gene trap ROSA 26, Philippe Soriano (NCBI Gene ID: 14910) is replaced to create Rosa26.mIre1.N906A.Cherry using the Loxed Cassette Acceptor allele Rosa26{tm1(LCA)}). This mouse contains bidirectional TetO-regulated genes inserted into the Rosa26.LCA allele by RMCE. In one direction the TetO/CMV promoter drives the expression of point mutant (N906A) of IRE1, an ER transmembrane kinase response to unfolded protein response (UPR). In the other direction it drives the expression of red fluorescent protein mCherry. This mouse can be used to simultaneously over-express Ire1 (N906A) and mCherry upon administration of doxycyline when the effector protein rtTA is expressed. This line can be used to study the roles of IRE1 in the response to ER stress, diet induced obesity and insulin resistance.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerRosa26{mIre1.N906A.CherryMgn}Vanderbilt University Medical CenterSst{rTTA.LCA.Mgn} mouse strainA mouse strain in which the targeted gene, Somatostatin (NCBI Gene ID: 20604), has been modified (allele type: Gene Replacement) to (MGI ID: Sst{rTTA.LCA}). TheSst.rTTA.LCA mice are designed to express a tet-inducible reverse-transactivator under control of somatostatin promoter. Lox66 and Lox2272 sites are inserted flanking 500bp of Sst promoter region, Sst exons I and II and Sst poly A site. The rTTA-beta-globin poly A cassete is put in place of Sst coding exons (I and II). The mice can be used to drive tet-inducible expression in somatostatin expressing cells (Delta-cells). Additionally, the Lox66 and Lox2272 sites allow for manipulations of the flanked region by RMCE in the future.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerSst{rTTA.LCA.Mgn}Vanderbilt University Medical CenterMonoclonal human ghrelin raised in mouseA monoclonal antibody raised in mouse that targets the human "ghrelin" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Gallbladder mucosal epithelium raised in mouseA monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Gallbladder mucosal epithelium raised in mouseA monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Gallbladder mucosal epithelium raised in mouseA monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Gallbladder mucosal epithelium raised in mouseA monoclonal antibody raised in mouse that targets the human "Gallbladder mucosal epithelium" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Alpha cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Alpha cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterMonoclonal human Pancreatic duct cells raised in mouseA monoclonal antibody raised in mouse that targets the human "Pancreatic duct cells" antigen.Person: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJ mouse strainA mouse strain that is immunodeficient and express human HLA class 1 heavy and light chains. This strain may be useful as a human hematopoietic engraftment host that supports the maturation of human T cells with transplantation http://jaxmice.jax.org/strain/014570.html. NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} Tg(HLA-A/H2-D/B2M)1Dvs/SzJPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterNOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJ mouse strainA mouse strain that lacks expression of the murine Prkdc gene, the X-linked Il2rg gene, and MHC class II, but express the human leukocyte antigen DR4 gene. These mice may be useful for targeting human CD4{+} T cells in transplantation studies in the absence of xeno-GVHD.More details are available at http://jaxmice.jax.org/strain/017637.html.NOD.Cg-Prkdc{scid} Il2rg{tm1Wjl} H2-Ab1{tm1Gru} Tg(HLA-DRB1)31Dmz/SzJPerson: Mark A. Magnuson, Jill Lindner, Jean-Philippe CartaillerVanderbilt University Medical CenterentityEntity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdfentityAn entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])EntityBFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81Julius CaesarVerdi’s Requiemthe Second World Waryour body mass indexAn entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])per discussion with Barry SmithEntity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdfcontinuant(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])Continuantcontinuant(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuantsif b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrentOccurrent(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] An entity that has temporal parts and that happens, unfolds or develops through time.An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial regionBFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])per discussion with Barry SmithOccurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])independent continuant(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])a chaira hearta moleculean orchestra.an organismb is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])icIndependentContinuanta lega spatial regionan atomthe bottom right portion of a human torsothe interior of your mouth(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] obsolete dependent continuanttrueA continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.spatial region(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])s-regionSpatialRegionA spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])BFO 2 Reference: Spatial regions do not participate in processes.Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])per discussion with Barry SmithSpatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] temporal region(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] t-region(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])TemporalRegionEvery temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensionalAll parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensionalper discussion with Barry Smith(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] two-dimensional spatial region2d-s-region(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] TwoDimensionalSpatialRegionA two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])an infinitely thin plane in space.the surface of a sphere-shaped part of spaceA two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] spatiotemporal region(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] SpatiotemporalRegionst-region(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])Every spatiotemporal region occupies_spatiotemporal_region itself.Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])the spatiotemporal region occupied by a human lifethe spatiotemporal region occupied by a process of cellular meiosis.the spatiotemporal region occupied by the development of a cancer tumor(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])processAn occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)a process of cell-division, \ a beating of the heartprocessProcess(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] a process of meiosisa process of sleepingp is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])the course of a diseasethe flight of a birdthe life of an organismyour process of aging.(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])dispositiondisposition(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] Disposition(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])an atom of element X has the disposition to decay to an atom of element Yb is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])certain people have a predisposition to colon cancerchildren are innately disposed to categorize objects in certain ways.the cell wall is disposed to filter chemicals in endocytosis and exocytosisIf b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable entity(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] RealizableEntityrealizableA specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])the disposition of this piece of metal to conduct electricity.the disposition of your blood to coagulatethe function of your reproductive organsthe role of being a doctorthe role of this boundary to delineate where Utah and Colorado meetTo say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] zero-dimensional spatial regionZeroDimensionalSpatialRegion(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] 0d-s-regionA zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] quality(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] Quality(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])qualityIf an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])the ambient temperature of this portion of airthe color of a tomatothe length of the circumference of your waistthe mass of this piece of gold.the shape of your nosethe shape of your nostril(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] specifically dependent continuant(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] sdc(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this keySpecifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.SpecificallyDependentContinuantb is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])of one-sided specifically dependent continuants: the mass of this tomatoof relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.the disposition of this fish to decaythe function of this heart: to pump bloodthe mutual dependence of proton donors and acceptors in chemical reactions [79the mutual dependence of the role predator and the role prey as played by two organisms in a given interactionthe pink color of a medium rare piece of grilled filet mignon at its centerthe role of being a doctorthe shape of this hole.the smell of this portion of mozzarella(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] per discussion with Barry SmithSpecifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])rolerole(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.Roleb is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])the priest rolethe role of a boundary to demarcate two neighboring administrative territoriesthe role of a building in serving as a military targetthe role of a stone in marking a property boundarythe role of subject in a clinical trialthe student role(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])fiat object(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisionsFiatObjectPartb is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])fiat-objector with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29the FMA:regional parts of an intact human body.the Western hemisphere of the Earththe division of the brain into regionsthe division of the planet into hemispheresthe dorsal and ventral surfaces of the bodythe upper and lower lobes of the left lung(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])one-dimensional spatial region(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] OneDimensionalSpatialRegion1d-s-regionA one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])an edge of a cube-shaped portion of space.(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])object aggregateobject-aggregateISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ObjectAggregateAn entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).a collection of cells in a blood biobank.a swarm of bees is an aggregate of members who are linked together through natural bondsa symphony orchestraan organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])defined by fiat: the aggregate of members of an organizationdefined through physical attachment: the aggregate of atoms in a lump of granitedefined through physical containment: the aggregate of molecules of carbon dioxide in a sealed containerdefined via attributive delimitations such as: the patients in this hospitalthe aggregate of bearings in a constant velocity axle jointthe aggregate of blood cells in your bodythe nitrogen atoms in the atmospherethe restaurants in Palo Altoyour collection of Meissen ceramic plates.An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] three-dimensional spatial region(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] 3d-s-regionThreeDimensionalSpatialRegionA three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])a cube-shaped region of spacea sphere-shaped region of space,A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] siteSite(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] a hole in the interior of a portion of cheesea rabbit holean air traffic control region defined in the airspace above an airportb is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])siteManhattan Canyon)the Grand Canyonthe Piazza San Marcothe cockpit of an aircraftthe hold of a shipthe interior of a kangaroo pouchthe interior of the trunk of your carthe interior of your bedroomthe interior of your officethe interior of your refrigeratorthe lumen of your gutyour left nostril (a fiat part – the opening – of your left nasal cavity)(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])objectBFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74ObjectobjectBFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).BFO 2 Reference: an object is a maximal causally unified material entityatomb is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])cellcells and organismsengineered artifactsgrain of sandmoleculeorganelleorganismplanetsolid portions of matterstarb is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])generically dependent continuantgdcGenericallyDependentContinuant(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])the pdf file on your laptop, the pdf file that is a copy thereof on my laptopthe sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] functionfunction(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.Functionthe function of a hammer to drive in nailsthe function of a heart pacemaker to regulate the beating of a heart through electricitythe function of amylase in saliva to break down starch into sugar(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])process boundaryProcessBoundaryp-boundary(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])the boundary between the 2nd and 3rd year of your life.(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] one-dimensional temporal region(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] 1d-t-regionA one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).OneDimensionalTemporalRegionthe temporal region during which a process occurs.(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])material entitymaterial(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] MaterialEntity(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])a flamea forest firea human beinga hurricanea photona puff of smokea sea wavea tornadoan aggregate of human beings.an energy wavean epidemicevery entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])the undetached arm of a human beingA material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])continuant fiat boundary(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.ContinuantFiatBoundaryEvery continuant fiat boundary is located at some spatial region at every time at which it existscf-boundaryBFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.immaterial entityimmaterialImmaterialEntityBFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10one-dimensional continuant fiat boundaryOneDimensionalContinuantFiatBoundary(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] 1d-cf-boundaryThe Equatora one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])all geopolitical boundariesall lines of latitude and longitudethe line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.the median sulcus of your tongue(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])process profile(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] ProcessProfileOne important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.process-profile(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levelsb is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])relational quality(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.RelationalQualitya marriage bond, an instance of love, an obligation between one person and another.b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])r-quality(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])two-dimensional continuant fiat boundary2d-cf-boundaryTwoDimensionalContinuantFiatBoundary(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] zero-dimensional continuant fiat boundary(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] 0d-cf-boundaryZeroDimensionalContinuantFiatBoundarya zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])the geographic North Polethe point of origin of some spatial coordinate system.the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meetzero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] requested by Melanie Courtotzero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.zero-dimensional temporal region0d-t-region(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])ZeroDimensionalTemporalRegiona temporal region that is occupied by a process boundaryright nowtemporal instant.the moment at which a child is bornthe moment at which a finger is detached in an industrial accidentthe moment of death.A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] historyA history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])HistoryhistoryA history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])insulinoma cellA cell of a usually benign tumor of the insulin-secreting cells of the pancreas.lymphoblastoid cell lineHuman cell line from tissue infected with Epstein-Barr virus, resembling a lymphoblast.embryonic stem cell linepancreatic ductal adenocarcinoma cellCCE cellCCE is a mouse embryonic stem cell line derived from 129/Sv mouse strain and has been provided for research use only.gross anatomical partAnatomical structure that is part of a multicellular organism and is at the gross anatomical level, e.g. above the level of a cell. Included are portions of organism substances such as blood, multi-cell-part structures such as axon tracts, acellular anatomical structures such as hair, and organism subdivisions such as head. Excluded is the whole organism and more granular parts of the organism, such as atoms, molecules, macromolecular complexes and cells.gross anatomical partbiotinAn organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins.biotinpolynucleotideA nucleobase-containing molecular entity with a polymeric structure comprised of a linear sequence of 13 or more nucleotide residues.polynucleotidepeptideAmide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.peptidedeoxyribonucleic acidHigh molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.deoxyribonucleic acidhydrogensulfiteA sulfur oxoanion that has formula HO3S.hydrogensulfitepolysaccharideA biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues.polysaccharide2'-deoxyribonucleoside2'-deoxyribonucleosidepyrimidine 2'-deoxyribonucleosidepyrimidine 2'-deoxyribonucleosideN-glycosyl compoundA glycosyl compound arising formally from the elimination of water from a glycosidic hydroxy group and an H atom bound to a nitrogen atom, thus creating a C-N bond.N-glycosyl compoundbenzopyrrolebenzopyrrolemolecular entityAny constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.molecular entitydeoxyribonucleosidedeoxyribonucleosidechemical entityA chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.chemical entityorganic heterocyclic compoundA cyclic compound having as ring members atoms of carbon and at least of one other element.organic heterocyclic compoundhydroxidesHydroxides are chemical compounds containing a hydroxy group or salts containing hydroxide (OH(-)).hydroxidesindolesAny compound containing an indole skeleton.indolesionA molecular entity having a net electric charge.ionagaroseagarosemoleculeAny polyatomic entity that is an electrically neutral entity consisting of more than one atom.moleculeorganic heteromonocyclic compoundorganic heteromonocyclic compoundoxideAn oxide is a chemical compound of oxygen with other chemical elements.oxideoxygen molecular entityoxygen molecular entitypyrimidine nucleosidepyrimidine nucleosidesulfur molecular entitysulfur molecular entityoxolanesAny oxacycle having an oxolane (tetrahydrofuran) skeleton.oxolanesorganic heterobicyclic compoundorganic heterobicyclic compoundphosphorus atomA pnictogen that has formula P.phosphorus atomatomA chemical entity constituting the smallest component of an element having the chemical properties of the element.atomprimary amideA derivative of an oxoacid RkE(=O)l(OH)m (l =/= 0) in which an acidic hydroxy group has been replaced by an amino or substituted amino group.primary amideorganosulfur compoundAn organosulfur compound is a compound containing at least one carbon-sulfur bond.organosulfur compoundpolyatomic anionAn anion consisting of more than one atom.polyatomic anionheteroorganic entityA heteroorganic entity is an organic molecular entity in which carbon atoms or organic groups are bonded directly to one or more heteroatoms.heteroorganic entitychalcogen molecular entityAny p-block molecular entity containing a chalcogen.chalcogen molecular entitymain group element atomAn atom belonging to one of the main groups (found in the s- and p- blocks) of the periodic table.main group element atomsulfur oxoacid derivativesulfur oxoacid derivativesulfur oxoanionsulfur oxoanionorganosulfonic acidAn organic derivative of sulfonic acid in which the sulfo group is linked directly to carbon.organosulfonic acidcarboxylic acidA carbon oxoacid acid carrying at least one -C(=O)OH group and having the structure RC(=O)OH, where R is any any monovalent functional group. Carboxylic acids are the most common type of organic acid.carboxylic acidmain group molecular entityA molecular entity containing one or more atoms from any of groups 1, 2, 13, 14, 15, 16, 17, and 18 of the periodic table.main group molecular entitycyclic compoundAny molecule that consists of a series of atoms joined together to form a ring.cyclic compoundorganic aromatic compoundorganic aromatic compoundheteromonocyclic compoundheteromonocyclic compoundheteropolycyclic compoundheteropolycyclic compoundheterobicyclic compoundA bicyclic compound in which at least one of the rings contains at least one skeletal heteroatom.heterobicyclic compoundp-block molecular entityA p-block molecular entity is a molecular entity containing one or more atoms of a p-block element.p-block molecular entitybiomacromoleculeA macromolecule formed by a living organism.biomacromoleculenucleic acidA macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.nucleic acidribonucleic acidHigh molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.ribonucleic acidorganic cyclic compoundAny organic molecule that consists of atoms connected in the form of a ring.organic cyclic compoundheteroareneA heterocyclic compound formally derived from an arene by replacement of one or more methine (-C=) and/or vinylene (-CH=CH-) groups by trivalent or divalent heteroatoms, respectively, in such a way as to maintain the continuous pi-electron system characteristic of aromatic systems and a number of out-of-plane pi-electrons corresponding to the Hueckel rule (4n+2).heteroarenenucleosideAn N-glycosyl compound that has both a nucleobase, normally adenine, guanine, xanthine, thymine, cytosine or uracil, and either a ribose or deoxyribose as functional parents.nucleosideorganonitrogen compoundAny heteroorganic entity containing at least one carbon-nitrogen bond.organonitrogen compoundoxoanionAn oxoanion is an anion derived from an oxoacid by loss of hydron(s) bound to oxygen.oxoanioncarbon oxoacidcarbon oxoacidpolyatomic entityAny molecular entity consisting of more than one atom.polyatomic entitypolyatomic ionAn ion consisting of more than one atom.polyatomic ioncarbonyl compoundAny compound containing the carbonyl group, C=O. The term is commonly used in the restricted sense of aldehydes and ketones, although it actually includes carboxylic acids and derivatives.carbonyl compoundorganochalcogen compoundAn organochalcogen compound is a compound containing at least one carbon-chalcogen bond.organochalcogen compoundorganooxygen compoundAn organochalcogen compound containing at least one carbon-oxygen bond.organooxygen compoundheteroatomic molecular entityA molecular entity consisting of two or more chemical elements.heteroatomic molecular entitycarboxamideAn amide of a carboxylic acid, having the structure RC(=O)NR2. The term is used as a suffix in systematic name formation to denote the -C(=O)NH2 group including its carbon atom.carboxamidecyanine dyeCyanine dyes are synthetic dyes with the general formula R2N[CH=CH]nCH=N(+)R2 <-> R2N(+)=CH[CH=CH]nNR2 (n is a small number) in which the nitrogen and part of the conjugated chain usually form part of a heterocyclic system, such as imidazole, pyridine, pyrrole, quinoline and thiazole.cyanine dyephosphorus-32 atomThe radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.phosphorus-32 atomphosphorus-33 atomThe radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.phosphorus-33 atomCy3 dyeCy3 dyeCy5 dyeCy5 dyeorganonitrogen heterocyclic compoundAny organonitrogen compound containing a cyclic component with nitrogen and at least one other element as ring member atoms.organonitrogen heterocyclic compoundoxacycleAny organic heterocyclic compound containing at least one ring oxygen atom.oxacycleorganosulfur heterocyclic compoundorganosulfur heterocyclic compoundorganic heteropentacyclic compoundorganic heteropentacyclic compoundorganic heteropolycyclic compoundorganic heteropolycyclic compoundazabicycloalkaneazabicycloalkanethiabicycloalkanethiabicycloalkanediazinesAny organic heterocyclic compound containing a benzene ring in which two of the C-H fragments have been replaced by isolobal nitrogens (the diazine parent structure).diazinesdouble-stranded DNAdouble-stranded DNA5-bromo-2'-deoxyuridine5-bromo-2'-deoxyuridineA pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase.organic molecular entityAny molecular entity that contains carbon.organic molecular entitynitrogen molecular entitynitrogen molecular entitybiotinsCompounds containing a biotin (5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid) skeleton.biotinsAlexa Fluor 532Alexa Fluor 532An organosulfonic acid that has formula C34H33N3O11S2.Alexa Fluor 546Alexa Fluor 546An organic heteropentacyclic compound that has formula C44H46Cl3N4NaO14S3.heterocyclic compoundA cyclic compound having as ring members atoms of at least two different elements.heterocyclic compoundnucleobase-containing molecular entityAny compound that has a nucleobase as a part.nucleobase-containing molecular entitypyrimidine deoxyribonucleosideA deoxyribonucleoside containing a pyrimidine base.pyrimidine deoxyribonucleosideorganic moleculeAny molecule that consists of at least one carbon atom as part of the electrically neutral entity.organic moleculecarbohydrates and carbohydrate derivativesAny organooxygen compound that is a polyhydroxy-aldehyde or -ketone, or a compound derived from one. Carbohydrates contain only carbon, hydrogen and oxygen and usually have an empirical formula Cm(H2O)n; carbohydrate derivatives may contain other elements by substitution or condensation.carbohydrates and carbohydrate derivativescell line cellA cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in cultureimmortal cell line cellA cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.cell lineA cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).immortal stem cell line cella cell line that is derived from stem cellimmortal neuron cell line cella immortal electrically responsive cell line cell that is derived from neuronimmortal animal cell line cella immortal eukaryotic cell line that is derived from animal cellimmortal hematopoietic cell line cella immortal animal cell line that is derived from hematopoietic cellimmortal neural cell line cella immortal animal cell line that is derived from neural cellimmortal somatic cell line cella cell line that is derived from somatic cellimmortal mouse embryo-derived cell line cellAn immortal embryo-derived cell line cell that derives from mouse.3T3-L1 cellAinv15 cellBETA-TC-3 cellCGR8 cellDaudi cellH9 cellJURKAT cellK 562 cellRaji cellSW480 cellimmortal cell lineA cell line that is expected to be capable of indefinite propagation in an vitro culture.cellA material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.CALOHA:TS-2035FMA:68646GO:0005623KUPO:0000002The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).VHOG:0001533WBbt:0004017XAO:0003012cellprimary cultured cellA cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged.BTO:0002290Covers cells actively being cultured or stored in a quiescent state for future use.cellprimary cell culture cellprimary cell line cellunpassaged cultured cellnative cellA cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment).CARO:0000013To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).cellcell in vivocultured cellA cell in vitro that is or has been maintained or propagated as part of a cell culture.Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. cellfemale germ cellFemale germ cell is a germ cell that supports female gamete production.MA:0000388VHOG:0001530cellncithesaurus:EggoocyteA female germ cell that has entered meiosis.BTO:0000964CALOHA:TS-0711FBbt:00004886FMA:18644WBbt:0006797celloogoniumstem cellA relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.CALOHA:TS-2086FMA:63368cellhematopoietic stem cellA stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119.BTO:0000725CALOHA:TS-0448FMA:70337FMA:86475HSCMarkers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.VHOG:0001485blood forming stem cellcellcolony forming unit hematopoietichemopoietic stem cellerythroid progenitor cellA progenitor cell committed to the erythroid lineage.BFU-EBTO:0004911CFU-Eblast forming unit erythroidburst forming unit erythroidcellcolony forming unit erythroiderythroid stem cellgerm line cellA cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring.Originally this term had some plant germ line cell children.cellmonoblastA myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus.CALOHA:TS-1195CFU-MFMA:83553Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.cellcolony forming unit macrophagecolony forming unit monocytemonocyte stem cellmulti fate stem cellA stem cell that can give rise to multiple lineages of cells.FMA:84789cellmulti-fate stem cellmultifate stem cellmultipotent cellmultipotent stem cellcommon myeloid progenitorA progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages.BTO:0004730CFU-GEMMCFU-SCMPcellcolony forming unit granulocyte, erythrocyte, macrophage, and megakaryocytecommon myeloid precursormultipotential myeloid stem cellmyeloid stem cellpluripotent stem cell (bone marrow)This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).megakaryocyte-erythroid progenitor cellA progenitor cell committed to the megakaryocyte and erythroid lineages.CFU-EMCFU-MegEMEPMEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.Meg/E progenitorcellcolony forming unit erythroid megakaryocytemegakaryocyte/erythrocyte progenitormegakaryocyte/erythroid progenitor cellcommon lymphoid progenitorA oligopotent progenitor cell committed to the lymphoid lineage.CL:0000044CLPCLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.ELPcellcommitted lymphopoietic stem cellcommon lymphocyte precursorcommon lymphocyte progenitorcommon lymphoid precursorearly lymphocyte progenitorlymphoid stem celllymphopoietic stem cellnon-terminally differentiated cellA precursor cell with a limited number of potential fates.BTO:0000125FMA:84782blast cellcelldefine using PATO mulit-potent or oligopotent?myoblastA cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair.BTO:0000222CALOHA:TS-0650FBbt:00005083FMA:70335VHOG:0001529cellfibroblastA connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.BTO:0000452CALOHA:TS-0362FMA:63877These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.VHOG:0001482cellepithelial cellA cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.BTO:0000414CALOHA:TS-2026CARO:0000077FBbt:00000124FMA:66768WBbt:0003672cellepitheliocyteduct epithelial cellcellbranched duct epithelial cellcellblood vessel endothelial cellAn endothelial cell that lines the vasculature.cellcuboidal endothelial cell of vascular treesquamous epithelial cellCALOHA:TS-1249cellblood cellA cell found predominately in the blood.FMA:62844cellepithelial cell of pancreasAn epithelial cell of the pancreas.BTO:0000028cellpancreatic epithelial cellpancreas epithelial cellT cellA type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.BTO:0000782CALOHA:TS-1001CL:0000804CL:0000812FMA:62870T lymphocyteT-cellT-lymphocyteVHOG:0001479cellimmature T cellmature T cellgranulocyteA leukocyte with abundant granules in the cytoplasm.BTO:0000539BTO:0001026CALOHA:TS-0422FMA:62854cellgranular leucocytegranular leukocytepolymorphonuclear leukocyteendothelial cellAn endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm.BTO:0001176CALOHA:TS-0278FMA:66772From FMA: 9.07.2001: Endothelial cell has always been classified as a kind of epithelial cell, specifically a squamous cell but that is not true. First, endothelial cell can either be squamous or cuboidal (e.g. high-endothelial cell) and secondly, it has different embryological derivation (mesodermal) than a true epithelial cell (ectodermal and endodermal). The basis for present classification is the fact that it comprises the outermost layer or lining of anatomical structures (location-based) but a better structural basis for the differentia is the cytoskeleton of the cell. Endothelial cell has vimentin filaments while an epithelial cell has keratin filaments. [Onard].cellendotheliocyteneurectodermal cellEctoderm destined to be nervous tissue.cellneurectoderm cellmesenchymal stem cellA connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. This cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs.BMSCBTO:0002625BTO:0003298CFU-FCL:0002452FMA:70546MSCMany but not all mesenchymal cells derive from the mesoderm. MSCs are reportedly CD3-negative, CD4-negative, CD5-negative, CD8-negative, CD11a-negative, CD11b-negative, CD14-negative, CD19-negative, CD29-positive, CD31-negative, CD34-negative, CD38-negative, CD40-negative, CD44-positive, CD45-negative, CD49-positive, CD54-positive, CD66b-negative, CD79a-negative, CD80-negative, CD102-positive, CD106-positive, CD117-positive, CD121a-positive, CD121b-positive, CD123-positive, CD124-positive, CD133-negative, CD146-positive, CD166-positive, CD271-positive, B220-negative, Gr1-negative, MHCI-positive, MHCII-negative, SSEA4-negative, sca1-positive, Ter119-negative, and glycophorin A-negative. Cultured MSCs are capable of producing stem cell factor, IL7, IL8, IL11, TGF-beta, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and MMP-2.bone marrow stromal cellscellcolony-forming unit-fibroblastmarrow stromal cellsmesenchymal precursor cellmesenchymal progenitor cellsmesenchymal stem cellmesenchymal stromal cellmesenchymal stromal cellsstem cells, mesenchymalfat cellA fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides.BTO:0000443CALOHA:TS-0012CL:0000450FMA:63880adipocyteadipose cellcellpigment cellA pigment cell is a cell that contains pigment granules.VHOG:0001678cellchromatocytechromatophoremelanocyteA pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance.BTO:0000847CALOHA:TS-0613CL:0000572FMA:70545VHOG:0001679cellmelanophoreglandular epithelial cellA specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules.CALOHA:TS-2085FMA:86494cellsecretory cellA cell that specializes in controlled release of one or more substances.BTO:0003659FMA:86916cellexocrine cellA cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct.FMA:16014cellprotein secreting cellcellendocrine cellA cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions.FMA:83809cellendocrinocyteenteroendocrine cellAn endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas.BTO:0003865FMA:62930cellpeptide hormone secreting cellcellinsulin secreting cellBTO:0000783celltype B pancreatic cellA cell that secretes insulin and is located towards the center of the islets of Langerhans.B-cell of pancreatic isletBTO:0000783EV:0200009FMA:70586MA:0002419Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression.beta cellbeta cell isletbeta cell of pancreatic isletcellinsulin-secreting cellncithesaurus:Beta_Cellpancreatic B cellpancreatic B-cellpancreatic beta cellpancreatic islet coretype B enteroendocrine cellglucagon secreting cellA cell that secretes glucagon.FMA:84045cellglucagon-secreting cellpancreatic A cellA type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon.BTO:0000990FMA:70585alpha cell of iselt of Langerhanscellpancreatic alpha cellsomatostatin secreting cellcellpancreatic D cellA D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin.BTO:0000803D-cell of pancreatic isletFMA:70587celldelta cell of isletdelta cell of pancreatic isletpancreatic D-cellpancreatic delta cellsomatostatin-secreting pancreatic cellmetabolising cellA cell whose primary function is intermediary metabolism.cellhepatocyteBTO:0000575CALOHA:TS-0454FMA:14515Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive.The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.cellcontractile cellA cell whose primary function is to shorten.cellmuscle cellA mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns.BTO:0000888BTO:0000902CALOHA:TS-2032FBbt:00005074FMA:67328WBbt:0003675cellmuscle fibermyocyteelectrically active cellA cell whose function is determined by the generation or the reception of an electric signal.celllining cellA cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism.boundary cellcellbarrier cellA cell whose primary function is to prevent the transport of stuff across compartments.cellmotile cellA cell that moves by its own activities.cellectodermal cellA cell of the outer of the three germ layers of the embryo.FMA:72549cellectoderm cellmesodermal cellA cell of the middle germ layer of the embryo.FMA:72554cellmesoblastmesoderm cellendodermal cellA cell of the inner of the three germ layers of the embryo.FMA:72555cellendoderm cellanucleate cellA cell that lacks a nucleus.FMA:68647cellnon-nucleated cellsingle nucleate cellA cell with a single nucleus.cellerythrocyteA red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.BTO:0000424CALOHA:TS-0290FMA:81100RBCcellred blood cellplateletA non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation.BTO:0000132CALOHA:TS-0803FMA:62851Platelets are reportedly CCR1-positive, CCR2-negative, CCR3-positive, CCR4-positive, CCR5-negative, CCR6-negative, CCR7-negative, CCR8-negative, CCR9-negative, CCR10-negative, CD16-positive, CD23-positive, CD32-positive, CD40-positive, CD41-positive CD42-positive, CD61-positive, CD62P-positive, CD64-positive, CD89-positive, CD102-positive, CD147-positive (activated platelets), CD154-positive (activated platelets), CD162-positive, CD209, CD282-positive, CD284-positive, CD289-positive, CD181-negative, CD182-negative, CD183-negative, CD184-positive, CLEC2-positive, GPVI-positive, JAMC-positive, PAR1-positive, PAR2-negative, PAR3-positive, PAR4-positive, TSP1-positive, and TXA2R-positive. Platelets can reportedly produce CCL2, CCL3, CCL5, CCL7, CCL17, CD40L, CXCL1, CXCL4, CXCL4L1, CXCL5, CXCL7, CXCL8, CXCL12, EGF, factor V, factor VII, factor XI, factor XIII, bFGF, histamine, IGF-1, IL-1beta, PAI-1, PDGF, plasminogen, protein S, serotonin, TGF-beta, TFPI, VEGF, and vWF.anucleate thrombocyteblood plateletcellenucleate thrombocyteB cellA lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity.B lymphocyteB-cellB-lymphocyteBTO:0000776CALOHA:TS-0068FMA:62869VHOG:0001480celleukaryotic cellcellstuff accumulating cellA cell that is specialised to accumulate a particular substance(s).celloxygen accumulating cellcellmigratory neural crest cellA cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body.FMA:86667cellelectrically responsive cellA cell whose function is determined by its response to an electric signal.cellpolyploid cellA cell whose nucleus, or nuclei, each contain more than two haploid genomes.cellendopolyploid cellcellwhite fat cellCALOHA:TS-1119FMA:83434Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole.cellwhite adipocytewhite adipose cellwhite fat celldendritic cellA cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative).BTO:0002042CALOHA:TS-0194FMA:83036cellinterdigitating cellveiled cellbiogenic amine secreting cellcellserotonin secreting cell5-HT secreting cell5-Hydroxytryptamine secreting cellA cell type that secretes 5-Hydroxytryptamine (serotonin).celltype D enteroendocrine cellA cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin.D cellFMA:62935cellcardiac muscle myoblastA precursor cell destined to differentiate into cardiac muscle cell.CL:0000714FMA:84797cellmelanoblastA cell that originates from the neural crest and differentiates into a pigment cell.BTO:0003217Derived from UBERON:0002342 neural crest.FMA:83377celllymphocyteA lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.BTO:0000775CALOHA:TS-0583Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)FMA:62863VHOG:0001535cellproerythroblastAn immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers.FMA:83518cellpronormoblastrubriblastanimal cellcellbasophilic erythroblastA nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers.FMA:83505basophilic normoblastcellearly erythroblastearly normoblastprorubricytepolychromatophilic erythroblastA nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers.FMA:83506cellintermediate erythroblastintermediate normoblastpolychromatic erythroblastpolychromatic normoblastpolychromatophilic normoblastrubricyteorthochromatic erythroblastFMA:84646The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated.acidophilic erythroblastcelleosinophilic erythroblastlate erythoblastorthochromatic normoblastpyknotic eto enrythroblastmegakaryocyte progenitor cellBTO:0001164CALOHA:TS-0610CFU-MegFMA:84235Lineage negative is described here as CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD14-negative, CD19-negative, CD20-negative, CD56-negative, Ly6g-negative, and Ter119-negative.Meg-CFCMkPThe earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative).cellcolony-forming unit-megakaryocytemegacaryoblastmegacaryocyte progenitor cellmegakaryoblastmegakaryocytic progenitor cellpromegacaryocytepromegakaryocytemegakaryocyteA giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm.BTO:0000843CALOHA:TS-0611FMA:83555Megakaryocytes are reportedly CD181-positive and CD182-positive.cellmegacaryocytemegalocaryocytemegalokaryocytegranulocyte monocyte progenitor cellA hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1.CFU-C , Colony forming unit in cultureCFU-GMGMPOriginally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative.cellcolony forming unit granulocyte macrophagegranulocyte-macrophage progenitorgranulocyte/monocyte precursorgranulocyte/monocyte progenitorreticulocyteAn immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds.BTO:0001173CALOHA:TS-0864cellpromonocyte